6-18486187-G-C

Variant names:

• chr6-18486187-G-C
• rs536700

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 0.934 in 152,238 control chromosomes in the GnomAD database, including 66,495 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 0.93 (66495 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.934 AC: 142140 AN: 152120 Hom.: 66439 Cov.: 31

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.934 AC: 142254 AN: 152238 Hom.: 66495 Cov.: 31 AF XY: 0.934 AC XY: 69543 AN XY: 74438

African (AFR) AF: 0.901 AC: 37418 AN: 41522

American (AMR) AF: 0.928 AC: 14184 AN: 15288

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

East Asian (EAS) AF: 0.954 AC: 4944 AN: 5180

South Asian (SAS) AF: 0.904 AC: 4362 AN: 4826

European-Finnish (FIN) AF: 0.962 AC: 10205 AN: 10610

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64688 AN: 68020

Other (OTH) AF: 0.930 AC: 1966 AN: 2114

Alfa AF: 0.950 Hom.: 3208

Bravo AF: 0.932

Asia WGS AF: 0.919 AC: 3199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs536700; hg19: chr6-18486418;