10-121677436-T-C

Variant names:

• chr10-121677436-T-C
• rs1696803

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 0.8 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

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.688 AC: 28498 AN: 41448

American (AMR) AF: 0.794 AC: 12120 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3041 AN: 3468

East Asian (EAS) AF: 0.868 AC: 4479 AN: 5160

South Asian (SAS) AF: 0.882 AC: 4246 AN: 4816

European-Finnish (FIN) AF: 0.903 AC: 9537 AN: 10566

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57032 AN: 67992

Other (OTH) AF: 0.808 AC: 1707 AN: 2112

Alfa AF: 0.828 Hom.: 25225

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
PhyloP100		-0.41

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Other links and lift over

dbSNP: rs1696803; hg19: chr10-123436950;