Variant chr10-41803908-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.506 in 151,736 control chromosomes in the GnomAD database, including 19,638 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 0.51 ( 19638 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

No conservation score assigned

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.506

AC:

76688

AN:

151618

Hom.:

19631

Cov.:

show subpopulations

Gnomad AFR

AF:

0.441

Gnomad AMI

AF:

0.552

Gnomad AMR

AF:

0.511

Gnomad ASJ

AF:

0.557

Gnomad EAS

AF:

0.425

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.473

Gnomad MID

AF:

0.459

Gnomad NFE

AF:

0.558

Gnomad OTH

AF:

0.519

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.506

AC:

76727

AN:

151736

Hom.:

19638

Cov.:

AF XY:

0.499

AC XY:

37020

AN XY:

74132

show subpopulations

Gnomad4 AFR

AF:

0.441

Gnomad4 AMR

AF:

0.511

Gnomad4 ASJ

AF:

0.557

Gnomad4 EAS

AF:

0.425

Gnomad4 SAS

AF:

0.406

Gnomad4 FIN

AF:

0.473

Gnomad4 NFE

AF:

0.558

Gnomad4 OTH

AF:

0.522

Alfa

AF:

0.545

Hom.:

40285

Bravo

AF:

0.508

Asia WGS

AF:

0.446

AC:

1549

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.6

DANN

Benign

0.81

Splicing

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