rs6796538

Variant names:

• chr3-10136836-A-G
• rs6796538

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 0.365 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.365 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

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0945

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.316

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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