chr10-92738679-T-C

Variant names:

• chr10-92738679-T-C
• rs4933236

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 0.425 in 151,940 control chromosomes in the GnomAD database, including 14,113 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 0.43 (14113 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64579 AN: 151820 Hom.: 14099 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.425 AC: 64639 AN: 151940 Hom.: 14113 Cov.: 31 AF XY: 0.429 AC XY: 31887 AN XY: 74270

African (AFR) AF: 0.433 AC: 17937 AN: 41434

American (AMR) AF: 0.445 AC: 6792 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1576 AN: 3466

East Asian (EAS) AF: 0.714 AC: 3672 AN: 5146

South Asian (SAS) AF: 0.569 AC: 2739 AN: 4816

European-Finnish (FIN) AF: 0.396 AC: 4177 AN: 10558

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26196 AN: 67954

Other (OTH) AF: 0.438 AC: 924 AN: 2108

Alfa AF: 0.406 Hom.: 35408

Bravo AF: 0.433

Asia WGS AF: 0.594 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.73
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs4933236; hg19: chr10-94498436;