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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFITM10	NM_001170820.4 link	c.-125A>G		5_prime_UTR_variant	Exon 1 of 3	ENST00000340134.5	NP_001164291.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFITM10	ENST00000340134.5 link	c.-125A>G		5_prime_UTR_variant	Exon 1 of 3	3	NM_001170820.4	ENSP00000344430.4
ENSG00000250644	ENST00000636615.1 link	c.1072-2448A>G		intron_variant	Intron 8 of 9	5		ENSP00000490014.1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over