6-18486256-T-A

Variant names:

• chr6-18486256-T-A
• rs490618

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 0.922 in 152,274 control chromosomes in the GnomAD database, including 64,791 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 0.92 (64791 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 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: 0.922 AC: 140223 AN: 152156 Hom.: 64745 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.922 AC: 140327 AN: 152274 Hom.: 64791 Cov.: 32 AF XY: 0.922 AC XY: 68612 AN XY: 74456

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.921

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.951

Gnomad4 OTH AF: 0.918

Alfa AF: 0.936 Hom.: 8287

Bravo AF: 0.917

Asia WGS AF: 0.914 AC: 3181 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	0.11
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs490618; hg19: chr6-18486487;