rs2647073

Variant names:

• chr6-32606237-A-C
• rs2647073

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 0.119 in 152,036 control chromosomes in the GnomAD database, including 1,200 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 0.12 (1200 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 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: 0.119 AC: 18124 AN: 151918 Hom.: 1204 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0423

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0506

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.119 AC: 18121 AN: 152036 Hom.: 1200 Cov.: 31 AF XY: 0.115 AC XY: 8568 AN XY: 74326

African (AFR) AF: 0.127 AC: 5251 AN: 41436

American (AMR) AF: 0.103 AC: 1573 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3464

East Asian (EAS) AF: 0.0426 AC: 221 AN: 5192

South Asian (SAS) AF: 0.165 AC: 793 AN: 4802

European-Finnish (FIN) AF: 0.0506 AC: 537 AN: 10606

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8802 AN: 67946

Other (OTH) AF: 0.133 AC: 281 AN: 2110

Alfa AF: 0.122 Hom.: 346

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.5
DANN	Benign	0.50
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs2647073; hg19: chr6-32574014;