10-41803908-C-T

Variant names:

• chr10-41803908-C-T
• rs10909011

Variant summary

Our verdict is Benign. Variant got -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

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

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

Other links and lift over

dbSNP: rs10909011; hg19: chr10-42436301;