rs378775

Variant names:

• chr6-52976681-C-G
• rs378775

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 0.735 in 152,082 control chromosomes in the GnomAD database, including 41,809 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 0.73 (41809 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 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: 0.735 AC: 111727 AN: 151964 Hom.: 41810 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.735 AC: 111756 AN: 152082 Hom.: 41809 Cov.: 31 AF XY: 0.736 AC XY: 54752 AN XY: 74344

African (AFR) AF: 0.604 AC: 25009 AN: 41436

American (AMR) AF: 0.664 AC: 10154 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2698 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4483 AN: 5170

South Asian (SAS) AF: 0.801 AC: 3863 AN: 4824

European-Finnish (FIN) AF: 0.807 AC: 8551 AN: 10590

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54462 AN: 67980

Other (OTH) AF: 0.747 AC: 1580 AN: 2116

Alfa AF: 0.753 Hom.: 5409

Bravo AF: 0.720

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.58
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs378775; hg19: chr6-52841479;