rs116638

Variant names:

• chr6-153940458-A-G
• rs116638

Your query was ambiguous. Multiple possible variants found:

• chr6-153940458-A-G
• chr6-153940458-A-T

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 0.57 in 151,956 control chromosomes in the GnomAD database, including 24,882 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 0.57 (24882 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.622 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: 0.570 AC: 86547 AN: 151836 Hom.: 24862 Cov.: 32

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.570 AC: 86602 AN: 151956 Hom.: 24882 Cov.: 32 AF XY: 0.567 AC XY: 42071 AN XY: 74256

African (AFR) AF: 0.515 AC: 21332 AN: 41408

American (AMR) AF: 0.491 AC: 7510 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2265 AN: 5146

South Asian (SAS) AF: 0.496 AC: 2386 AN: 4812

European-Finnish (FIN) AF: 0.640 AC: 6750 AN: 10540

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42592 AN: 67974

Other (OTH) AF: 0.566 AC: 1196 AN: 2112

Alfa AF: 0.577 Hom.: 3144

Bravo AF: 0.561

Asia WGS AF: 0.423 AC: 1474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.90
DANN	Benign	0.33
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs116638; hg19: chr6-154261593;