18-62393502-A-G

Variant names:

• chr18-62393502-A-G
• rs2957128

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 0.558 in 151,996 control chromosomes in the GnomAD database, including 24,372 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 0.56 (24372 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 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: 0.559 AC: 84832 AN: 151878 Hom.: 24366 Cov.: 31

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.558 AC: 84871 AN: 151996 Hom.: 24372 Cov.: 31 AF XY: 0.549 AC XY: 40761 AN XY: 74294

African (AFR) AF: 0.605 AC: 25074 AN: 41416

American (AMR) AF: 0.544 AC: 8318 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3470

East Asian (EAS) AF: 0.239 AC: 1236 AN: 5166

South Asian (SAS) AF: 0.563 AC: 2713 AN: 4820

European-Finnish (FIN) AF: 0.417 AC: 4408 AN: 10562

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39018 AN: 67954

Other (OTH) AF: 0.592 AC: 1250 AN: 2110

Alfa AF: 0.570 Hom.: 113378

Bravo AF: 0.568

Asia WGS AF: 0.404 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.40
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs2957128; hg19: chr18-60060735;