rs6919857

Variant names:

• chr6-136819316-C-T
• rs6919857

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 0.65 in 152,112 control chromosomes in the GnomAD database, including 32,544 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 0.65 (32544 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.532
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.751 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: 0.650 AC: 98797 AN: 151994 Hom.: 32528 Cov.: 33

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.650 AC: 98854 AN: 152112 Hom.: 32544 Cov.: 33 AF XY: 0.645 AC XY: 47969 AN XY: 74342

African (AFR) AF: 0.758 AC: 31468 AN: 41508

American (AMR) AF: 0.682 AC: 10435 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2191 AN: 3468

East Asian (EAS) AF: 0.496 AC: 2561 AN: 5164

South Asian (SAS) AF: 0.554 AC: 2674 AN: 4828

European-Finnish (FIN) AF: 0.548 AC: 5784 AN: 10554

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41809 AN: 67976

Other (OTH) AF: 0.633 AC: 1340 AN: 2116

Alfa AF: 0.628 Hom.: 38238

Bravo AF: 0.662

Asia WGS AF: 0.550 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.6
DANN	Benign	0.68
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs6919857; hg19: chr6-137140454;