10-121677436-T-C

Variant names:

• chr10-121677436-T-C
• rs1696803

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 0.8 in 152,028 control chromosomes in the GnomAD database, including 49,130 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 0.80 (49130 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

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 (SAS) allele frequency at 95% confidence interval = 0.86 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: 0.800 AC: 121525 AN: 151910 Hom.: 49075 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.826

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.800 AC: 121644 AN: 152028 Hom.: 49130 Cov.: 31 AF XY: 0.805 AC XY: 59793 AN XY: 74312

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.877

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.808

Alfa AF: 0.827 Hom.: 14661

Bravo AF: 0.786

Asia WGS AF: 0.860 AC: 2987 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	3.2
DANN	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1696803; hg19: chr10-123436950;