rs376819

Variant names:

• chr6-94314662-A-T
• rs376819

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;