6-36665292-A-G

Variant names:

• chr6-36665292-A-G
• rs4713999

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 151,930 control chromosomes in the GnomAD database, including 31,779 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 (31779 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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: 0.644 AC: 97835 AN: 151812 Hom.: 31754 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.644 AC: 97896 AN: 151930 Hom.: 31779 Cov.: 31 AF XY: 0.644 AC XY: 47860 AN XY: 74260

Gnomad4 AFR AF: 0.620

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.617

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.653

Gnomad4 OTH AF: 0.589

Alfa AF: 0.627 Hom.: 15183

Bravo AF: 0.646

Asia WGS AF: 0.639 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713999; hg19: chr6-36633069;