chr6-147484313-C-A

Variant names:

• chr6-147484313-C-A
• rs325124

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 0.603 in 152,040 control chromosomes in the GnomAD database, including 29,694 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 0.60 (29694 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 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: 0.603 AC: 91604 AN: 151922 Hom.: 29676 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.603 AC: 91679 AN: 152040 Hom.: 29694 Cov.: 32 AF XY: 0.601 AC XY: 44677 AN XY: 74330

African (AFR) AF: 0.352 AC: 14601 AN: 41426

American (AMR) AF: 0.625 AC: 9556 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2276 AN: 3468

East Asian (EAS) AF: 0.528 AC: 2727 AN: 5168

South Asian (SAS) AF: 0.617 AC: 2975 AN: 4824

European-Finnish (FIN) AF: 0.688 AC: 7266 AN: 10558

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49952 AN: 67990

Other (OTH) AF: 0.635 AC: 1342 AN: 2112

Alfa AF: 0.552 Hom.: 2036

Bravo AF: 0.586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.23
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs325124; hg19: chr6-147805449;