rs6796538

Variant names:

• chr3-10136836-A-G
• rs6796538

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 0.365 in 152,250 control chromosomes in the GnomAD database, including 14,155 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 0.37 (14155 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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: 0.365 AC: 55532 AN: 152132 Hom.: 14140 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.365 AC: 55591 AN: 152250 Hom.: 14155 Cov.: 33 AF XY: 0.356 AC XY: 26481 AN XY: 74456

African (AFR) AF: 0.732 AC: 30418 AN: 41534

American (AMR) AF: 0.250 AC: 3821 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3472

East Asian (EAS) AF: 0.0945 AC: 490 AN: 5186

South Asian (SAS) AF: 0.240 AC: 1158 AN: 4828

European-Finnish (FIN) AF: 0.159 AC: 1687 AN: 10602

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15977 AN: 68000

Other (OTH) AF: 0.316 AC: 668 AN: 2116

Alfa AF: 0.314 Hom.: 1270

Bravo AF: 0.389

Asia WGS AF: 0.178 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.10
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6796538; hg19: chr3-10178520; COSMIC: COSV56560995;