rs1595273

chr18-40697151-G-Achr18-40697151-G-Cchr18-40697151-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 0.346 in 151,948 control chromosomes in the GnomAD database, including 9,989 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 0.35 (9989 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 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: 0.346 AC: 52575 AN: 151830 Hom.: 9983 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.346 AC: 52612 AN: 151948 Hom.: 9989 Cov.: 32 AF XY: 0.357 AC XY: 26518 AN XY: 74248

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.357

Alfa AF: 0.244 Hom.: 859

Bravo AF: 0.344

Asia WGS AF: 0.688 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.014
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1595273; hg19: chr18-38277115;