rs12662737

Variant names:

• chr6-66564807-A-G
• rs12662737

Your query was ambiguous. Multiple possible variants found:

• chr6-66564807-A-G
• chr6-66564807-A-T

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 0.607 in 151,886 control chromosomes in the GnomAD database, including 28,225 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 0.61 (28225 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.736 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: 0.607 AC: 92088 AN: 151768 Hom.: 28196 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.607 AC: 92166 AN: 151886 Hom.: 28225 Cov.: 32 AF XY: 0.611 AC XY: 45326 AN XY: 74204

African (AFR) AF: 0.568 AC: 23541 AN: 41428

American (AMR) AF: 0.613 AC: 9346 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2246 AN: 3470

East Asian (EAS) AF: 0.586 AC: 3009 AN: 5136

South Asian (SAS) AF: 0.756 AC: 3647 AN: 4824

European-Finnish (FIN) AF: 0.609 AC: 6429 AN: 10550

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41893 AN: 67928

Other (OTH) AF: 0.600 AC: 1266 AN: 2110

Alfa AF: 0.618 Hom.: 23124

Bravo AF: 0.602

Asia WGS AF: 0.698 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.44
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs12662737; hg19: chr6-67274700;