rs12662737

chr6-66564807-A-Gchr6-66564807-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 0.607 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.600

Alfa AF: 0.620 Hom.: 19605

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12662737; hg19: chr6-67274700;