dbSNP rs3740621: IFITM10:c.-125A>G (chr11-1750567-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001170820.4(IFITM10):c.-125A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,243,332 control chromosomes in the GnomAD database, including 45,360 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 0.32 ( 9710 hom., cov: 31)

Exomes 𝑓: 0.25 ( 35650 hom. )

Consequence

IFITM10
NM_001170820.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.15

Publications

10 publications found

Variant links:

Genes affected

IFITM10 (HGNC:40022): (interferon induced transmembrane protein 10) Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

IFITM10 links:

ENSG00000250644 (HGNC:):

ENSG00000250644 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001170820.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFITM10	NM_001170820.4	MANE Select	c.-125A>G		5_prime_UTR	Exon 1 of 3	NP_001164291.2	A6NMD0

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IFITM10	ENST00000340134.5	TSL:3 MANE Select	c.-125A>G	5_prime_UTR	Exon 1 of 3	ENSP00000344430.4	A6NMD0
ENSG00000250644	ENST00000636615.1	TSL:5	c.1072-2448A>G	intron	N/A	ENSP00000490014.1	A0A1B0GU92
IFITM10	ENST00000902500.1		c.-125A>G	5_prime_UTR	Exon 1 of 3	ENSP00000572559.1

Frequencies

GnomAD3 genomes

AF:

0.323

AC:

49074

AN:

151786

Hom.:

9685

Cov.:

show subpopulations

Gnomad AFR

AF:

0.554

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.266

Gnomad ASJ

AF:

0.336

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.241

Gnomad FIN

AF:

0.145

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.242

Gnomad OTH

AF:

0.318

GnomAD4 exome

AF:

0.247

AC:

269392

AN:

1091430

Hom.:

35650

Cov.:

AF XY:

0.246

AC XY:

133629

AN XY:

543890

show subpopulations

African (AFR)

AF:

0.567

AC:

14532

AN:

25614

American (AMR)

AF:

0.221

AC:

6901

AN:

31284

Ashkenazi Jewish (ASJ)

AF:

0.330

AC:

6562

AN:

19878

East Asian (EAS)

AF:

0.215

AC:

7344

AN:

34180

South Asian (SAS)

AF:

0.233

AC:

15218

AN:

65308

European-Finnish (FIN)

AF:

0.165

AC:

6331

AN:

38328

Middle Eastern (MID)

AF:

0.370

AC:

1841

AN:

4970

European-Non Finnish (NFE)

AF:

0.240

AC:

197816

AN:

824382

Other (OTH)

AF:

0.271

AC:

12847

AN:

47486

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

10455

20910

31365

41820

52275

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6464

12928

19392

25856

32320

<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:

0.324

AC:

49156

AN:

151902

Hom.:

9710

Cov.:

AF XY:

0.316

AC XY:

23437

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.555

AC:

22930

AN:

41326

American (AMR)

AF:

0.266

AC:

4069

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.336

AC:

1165

AN:

3468

East Asian (EAS)

AF:

0.192

AC:

990

AN:

5154

South Asian (SAS)

AF:

0.240

AC:

1154

AN:

4812

European-Finnish (FIN)

AF:

0.145

AC:

1535

AN:

10592

Middle Eastern (MID)

AF:

0.364

AC:

107

AN:

294

European-Non Finnish (NFE)

AF:

0.242

AC:

16440

AN:

67958

Other (OTH)

AF:

0.318

AC:

672

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1491

2982

4473

5964

7455

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

444

888

1332

1776

2220

<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:

0.274

Hom.:

13928

Bravo

AF:

0.341

Asia WGS

AF:

0.248

AC:

864

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.28

(source)

DANN

Benign

0.45

PhyloP100

-2.2

PromoterAI

-0.039

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.99

Mutation Taster

=300/0

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