rs2647044

Variant names:

• chr6-32700133-G-A
• rs2647044

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 0.103 in 145,496 control chromosomes in the GnomAD database, including 933 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 0.10 (933 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 56 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 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: 0.103 AC: 14946 AN: 145396 Hom.: 931 Cov.: 29

Gnomad AFR AF: 0.0810

Gnomad AMI AF: 0.0598

Gnomad AMR AF: 0.0749

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.0524

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0941

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0955

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

GnomAD4 genome AF: 0.103 AC: 14961 AN: 145496 Hom.: 933 Cov.: 29 AF XY: 0.101 AC XY: 7134 AN XY: 70724

African (AFR) AF: 0.0811 AC: 3250 AN: 40072

American (AMR) AF: 0.0748 AC: 1013 AN: 13548

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 203 AN: 3298

East Asian (EAS) AF: 0.0523 AC: 250 AN: 4776

South Asian (SAS) AF: 0.122 AC: 571 AN: 4666

European-Finnish (FIN) AF: 0.0941 AC: 897 AN: 9528

Middle Eastern (MID) AF: 0.123 AC: 35 AN: 284

European-Non Finnish (NFE) AF: 0.128 AC: 8498 AN: 66422

Other (OTH) AF: 0.0945 AC: 192 AN: 2032

Alfa AF: 0.124 Hom.: 1522

Bravo AF: 0.0943

Asia WGS AF: 0.0560 AC: 189 AN: 3380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.75
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2647044; hg19: chr6-32667910;