rs2647045

Positions:

• chr6-32700323-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.286

Alfa AF: 0.241 Hom.: 561

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2647045; hg19: chr6-32668100;