rs594930

Variant names:

• chr6-113849240-C-T
• rs594930

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 0.902 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.902 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

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.950

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.971

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.925

Alfa AF: 0.947 Hom.: 89518

Bravo AF: 0.894

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs594930; hg19: chr6-114170427;