rs594930

Variant names:

• chr6-113849240-C-T
• rs594930

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 0.902 in 152,248 control chromosomes in the GnomAD database, including 62,556 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 0.90 (62556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.561
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.902 AC: 137235 AN: 152130 Hom.: 62523 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.981

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.957

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.902 AC: 137321 AN: 152248 Hom.: 62556 Cov.: 32 AF XY: 0.905 AC XY: 67385 AN XY: 74444

African (AFR) AF: 0.751 AC: 31164 AN: 41500

American (AMR) AF: 0.950 AC: 14541 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3366 AN: 3472

East Asian (EAS) AF: 0.974 AC: 5053 AN: 5186

South Asian (SAS) AF: 0.966 AC: 4653 AN: 4818

European-Finnish (FIN) AF: 0.971 AC: 10314 AN: 10620

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65114 AN: 68032

Other (OTH) AF: 0.925 AC: 1954 AN: 2112

Alfa AF: 0.941 Hom.: 110779

Bravo AF: 0.894

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs594930; hg19: chr6-114170427;