rs376819

Variant names:

• chr6-94314662-A-T
• rs376819

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 0.133 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.298 AC: 12328 AN: 41432

American (AMR) AF: 0.0844 AC: 1288 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0840 AC: 291 AN: 3466

East Asian (EAS) AF: 0.0520 AC: 269 AN: 5176

South Asian (SAS) AF: 0.0907 AC: 437 AN: 4820

European-Finnish (FIN) AF: 0.0395 AC: 419 AN: 10620

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0695 AC: 4722 AN: 67922

Other (OTH) AF: 0.120 AC: 253 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.7
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs376819; hg19: chr6-95024380;