rs597503

chr18-6939948-G-Achr18-6939948-G-Cchr18-6939948-G-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 0.859 in 152,258 control chromosomes in the GnomAD database, including 56,312 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 0.86 (56312 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.625

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 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: 0.859 AC: 130674 AN: 152140 Hom.: 56283 Cov.: 33

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.859 AC: 130762 AN: 152258 Hom.: 56312 Cov.: 33 AF XY: 0.860 AC XY: 64024 AN XY: 74450

Gnomad4 AFR AF: 0.822

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.836

Gnomad4 SAS AF: 0.825

Gnomad4 FIN AF: 0.949

Gnomad4 NFE AF: 0.875

Gnomad4 OTH AF: 0.846

Alfa AF: 0.867 Hom.: 64079

Bravo AF: 0.851

Asia WGS AF: 0.837 AC: 2910 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.5
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs597503; hg19: chr18-6939947;