rs2647045

Variant names:

• chr6-32700323-G-A
• rs2647045

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 0.273 in 151,942 control chromosomes in the GnomAD database, including 6,041 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 0.27 (6041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.622
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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: 0.273 AC: 41468 AN: 151824 Hom.: 6035 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.273 AC: 41498 AN: 151942 Hom.: 6041 Cov.: 32 AF XY: 0.281 AC XY: 20859 AN XY: 74264

African (AFR) AF: 0.251 AC: 10408 AN: 41422

American (AMR) AF: 0.387 AC: 5917 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1213 AN: 3462

East Asian (EAS) AF: 0.418 AC: 2158 AN: 5164

South Asian (SAS) AF: 0.380 AC: 1827 AN: 4808

European-Finnish (FIN) AF: 0.297 AC: 3132 AN: 10540

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15950 AN: 67962

Other (OTH) AF: 0.286 AC: 604 AN: 2112

Alfa AF: 0.257 Hom.: 1573

Bravo AF: 0.284

Asia WGS AF: 0.347 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.1
DANN	Benign	0.57
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs2647045; hg19: chr6-32668100;