Genetic Variant NM_017911.4:c.-9-211A>G (chr22-45322160-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017911.4(FAM118A):c.-9-211A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 1,490,466 control chromosomes in the GnomAD database, including 89,548 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 18241 hom., cov: 32)

Exomes 𝑓: 0.31 ( 71307 hom. )

Consequence

FAM118A
NM_017911.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.245

Publications

17 publications found

Variant links:

Genes affected

FAM118A (HGNC:1313): (family with sequence similarity 118 member A) Enables identical protein binding activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

FAM118A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017911.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FAM118A	NM_017911.4	MANE Select	c.-9-211A>G	intron	N/A	NP_060381.2
FAM118A	NR_146323.1		n.1158A>G	non_coding_transcript_exon	Exon 4 of 12
FAM118A	NM_001349916.2		c.-23A>G	5_prime_UTR	Exon 3 of 11	NP_001336845.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FAM118A	ENST00000441876.7	TSL:1 MANE Select	c.-9-211A>G	intron	N/A	ENSP00000395892.2
FAM118A	ENST00000452238.5	TSL:5	c.-23A>G	5_prime_UTR	Exon 3 of 4	ENSP00000388511.1
FAM118A	ENST00000424557.1	TSL:4	c.-23A>G	5_prime_UTR	Exon 3 of 4	ENSP00000389298.1

Frequencies

GnomAD3 genomes

AF:

0.443

AC:

67257

AN:

151810

Hom.:

18202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.759

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.429

Gnomad ASJ

AF:

0.325

Gnomad EAS

AF:

0.474

Gnomad SAS

AF:

0.470

Gnomad FIN

AF:

0.299

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.419

GnomAD2 exomes

AF:

0.371

AC:

55655

AN:

149838

AF XY:

0.374

show subpopulations

Gnomad AFR exome

AF:

0.779

Gnomad AMR exome

AF:

0.381

Gnomad ASJ exome

AF:

0.345

Gnomad EAS exome

AF:

0.492

Gnomad FIN exome

AF:

0.288

Gnomad NFE exome

AF:

0.287

Gnomad OTH exome

AF:

0.367

GnomAD4 exome

AF:

0.310

AC:

414887

AN:

1338542

Hom.:

71307

Cov.:

AF XY:

0.313

AC XY:

206239

AN XY:

659236

show subpopulations

African (AFR)

AF:

0.781

AC:

23544

AN:

30136

American (AMR)

AF:

0.385

AC:

12853

AN:

33380

Ashkenazi Jewish (ASJ)

AF:

0.336

AC:

7838

AN:

23314

East Asian (EAS)

AF:

0.462

AC:

14481

AN:

31314

South Asian (SAS)

AF:

0.450

AC:

34799

AN:

77272

European-Finnish (FIN)

AF:

0.290

AC:

12208

AN:

42082

Middle Eastern (MID)

AF:

0.448

AC:

2418

AN:

5396

European-Non Finnish (NFE)

AF:

0.276

AC:

287512

AN:

1041274

Other (OTH)

AF:

0.354

AC:

19234

AN:

54374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

11654

23309

34963

46618

58272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10242

20484

30726

40968

51210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.443

AC:

67356

AN:

151924

Hom.:

18241

Cov.:

AF XY:

0.444

AC XY:

32943

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.759

AC:

31441

AN:

41410

American (AMR)

AF:

0.429

AC:

6548

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.325

AC:

1126

AN:

3468

East Asian (EAS)

AF:

0.475

AC:

2447

AN:

5152

South Asian (SAS)

AF:

0.470

AC:

2259

AN:

4806

European-Finnish (FIN)

AF:

0.299

AC:

3160

AN:

10578

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.282

AC:

19128

AN:

67936

Other (OTH)

AF:

0.424

AC:

895

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1580

3160

4740

6320

7900

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

580

1160

1740

2320

2900

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.440

Hom.:

8019

Bravo

AF:

0.464

Asia WGS

AF:

0.516

AC:

1796

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.1

(source)

DANN

Benign

0.35

PhyloP100

-0.24

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over