rs2647046

Positions:

• chr6-32700559-A-C
• chr6-32700559-A-G
• chr6-32700559-A-T

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 0.644 in 151,598 control chromosomes in the GnomAD database, including 31,916 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 0.64 (31916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.992

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97628 AN: 151480 Hom.: 31894 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.772

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.644 AC: 97702 AN: 151598 Hom.: 31916 Cov.: 32 AF XY: 0.649 AC XY: 48101 AN XY: 74114

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.772

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.689

Alfa AF: 0.571 Hom.: 3719

Bravo AF: 0.656

Asia WGS AF: 0.769 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2647046; hg19: chr6-32668336;