chr6-32700559-A-C

Variant names:

• chr6-32700559-A-C
• rs2647046

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 0.644 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
• Publications: 39 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.634 AC: 26154 AN: 41282

American (AMR) AF: 0.740 AC: 11306 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.772 AC: 2671 AN: 3458

East Asian (EAS) AF: 0.818 AC: 4198 AN: 5132

South Asian (SAS) AF: 0.680 AC: 3269 AN: 4810

European-Finnish (FIN) AF: 0.654 AC: 6871 AN: 10508

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40875 AN: 67824

Other (OTH) AF: 0.689 AC: 1453 AN: 2110

Alfa AF: 0.625 Hom.: 13986

Bravo AF: 0.656

Asia WGS AF: 0.769 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.55
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs2647046; hg19: chr6-32668336;