10-41803908-C-T

Variant names:

• chr10-41803908-C-T
• rs10909011

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76688 AN: 151618 Hom.: 19631 Cov.: 32

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.: 32 AF XY: 0.499 AC XY: 37020 AN XY: 74132

African (AFR) AF: 0.441 AC: 18246 AN: 41356

American (AMR) AF: 0.511 AC: 7778 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1931 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2180 AN: 5132

South Asian (SAS) AF: 0.406 AC: 1951 AN: 4804

European-Finnish (FIN) AF: 0.473 AC: 4976 AN: 10518

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37931 AN: 67920

Other (OTH) AF: 0.522 AC: 1100 AN: 2108

Alfa AF: 0.538 Hom.: 62840

Bravo AF: 0.508

Asia WGS AF: 0.446 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

Other links and lift over

dbSNP: rs10909011; hg19: chr10-42436301;