rs490618

Variant names:

• chr6-18486256-T-A
• rs490618

Your query was ambiguous. Multiple possible variants found:

• chr6-18486256-T-A
• chr6-18486256-T-C
• chr6-18486256-T-G

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 0.922 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.858 AC: 35627 AN: 41540

American (AMR) AF: 0.921 AC: 14089 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3314 AN: 3472

East Asian (EAS) AF: 0.955 AC: 4943 AN: 5178

South Asian (SAS) AF: 0.904 AC: 4360 AN: 4822

European-Finnish (FIN) AF: 0.962 AC: 10208 AN: 10614

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64678 AN: 68028

Other (OTH) AF: 0.918 AC: 1936 AN: 2110

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs490618; hg19: chr6-18486487;