rs6796538

chr3-10136836-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;