rs4947339

Variant names:

• chr6-28948475-C-T
• rs4947339

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 0.566 in 151,828 control chromosomes in the GnomAD database, including 27,180 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 0.57 (27180 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.848 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: 0.565 AC: 85778 AN: 151710 Hom.: 27118 Cov.: 32

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.566 AC: 85886 AN: 151828 Hom.: 27180 Cov.: 32 AF XY: 0.568 AC XY: 42130 AN XY: 74196

African (AFR) AF: 0.855 AC: 35479 AN: 41474

American (AMR) AF: 0.552 AC: 8405 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1969 AN: 3468

East Asian (EAS) AF: 0.651 AC: 3371 AN: 5176

South Asian (SAS) AF: 0.623 AC: 3006 AN: 4824

European-Finnish (FIN) AF: 0.381 AC: 4009 AN: 10534

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.410 AC: 27786 AN: 67802

Other (OTH) AF: 0.587 AC: 1239 AN: 2110

Alfa AF: 0.474 Hom.: 47071

Bravo AF: 0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.13
DANN	Benign	0.75
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs4947339; hg19: chr6-28916252;