rs594930

chr6-113849240-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;