Variant chr11-1750567-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
IFITM10	NM_001170820.4 linkuse as main transcript	c.-125A>G		5_prime_UTR_variant	1/3	ENST00000340134.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFITM10	ENST00000340134.5 linkuse as main transcript	c.-125A>G		5_prime_UTR_variant	1/3	3	NM_001170820.4	P1
IFITM10	ENST00000382123.1 linkuse as main transcript	c.-125A>G		5_prime_UTR_variant, NMD_transcript_variant	1/4	3

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

Gnomad4 AFR exome

AF:

0.567

Gnomad4 AMR exome

AF:

0.221

Gnomad4 ASJ exome

AF:

0.330

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.233

Gnomad4 FIN exome

AF:

0.165

Gnomad4 NFE exome

AF:

0.240

Gnomad4 OTH exome

AF:

0.271

GnomAD4 genome

AF:

0.324

AC:

49156

AN:

151902

Hom.:

9710

Cov.:

AF XY:

0.316

AC XY:

23437

AN XY:

74252

show subpopulations

Gnomad4 AFR

AF:

0.555

Gnomad4 AMR

AF:

0.266

Gnomad4 ASJ

AF:

0.336

Gnomad4 EAS

AF:

0.192

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.145

Gnomad4 NFE

AF:

0.242

Gnomad4 OTH

AF:

0.318

Alfa

AF:

0.259

Hom.:

6933

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

DANN

Benign

0.45

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

0.99

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over