rs6919857

Positions:

• chr6-136819316-C-T

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 0.65 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.758

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.633

Alfa AF: 0.621 Hom.: 28466

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6919857; hg19: chr6-137140454;