rs376819

Positions:

• chr6-94314662-A-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 0.133 in 152,016 control chromosomes in the GnomAD database, including 2,130 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 0.13 (2130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 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: 0.132 AC: 20101 AN: 151898 Hom.: 2113 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.0840

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.0395

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.133 AC: 20152 AN: 152016 Hom.: 2130 Cov.: 32 AF XY: 0.130 AC XY: 9625 AN XY: 74296

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.0844

Gnomad4 ASJ AF: 0.0840

Gnomad4 EAS AF: 0.0520

Gnomad4 SAS AF: 0.0907

Gnomad4 FIN AF: 0.0395

Gnomad4 NFE AF: 0.0695

Gnomad4 OTH AF: 0.120

Alfa AF: 0.106 Hom.: 173

Bravo AF: 0.143

Asia WGS AF: 0.0990 AC: 346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
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: rs376819; hg19: chr6-95024380;