rs12664598

Variant names:

• chr6-40833992-A-G
• rs12664598

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 0.051 in 152,182 control chromosomes in the GnomAD database, including 282 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 0.051 (282 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0607 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: 0.0510 AC: 7756 AN: 152064 Hom.: 283 Cov.: 32

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0510 AC: 7757 AN: 152182 Hom.: 282 Cov.: 32 AF XY: 0.0537 AC XY: 3998 AN XY: 74390

African (AFR) AF: 0.0133 AC: 554 AN: 41544

American (AMR) AF: 0.0292 AC: 446 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3470

East Asian (EAS) AF: 0.0551 AC: 285 AN: 5174

South Asian (SAS) AF: 0.0220 AC: 106 AN: 4822

European-Finnish (FIN) AF: 0.144 AC: 1525 AN: 10574

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0623 AC: 4235 AN: 68006

Other (OTH) AF: 0.0545 AC: 115 AN: 2112

Alfa AF: 0.0570 Hom.: 476

Bravo AF: 0.0429

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs12664598; hg19: chr6-40801731;