rs770238

Variant names:

• chr18-2527969-C-A
• rs770238

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 0.491 in 151,956 control chromosomes in the GnomAD database, including 19,257 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 0.49 (19257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 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: 0.491 AC: 74552 AN: 151838 Hom.: 19232 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.491 AC: 74616 AN: 151956 Hom.: 19257 Cov.: 32 AF XY: 0.492 AC XY: 36529 AN XY: 74260

African (AFR) AF: 0.638 AC: 26432 AN: 41420

American (AMR) AF: 0.422 AC: 6443 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3464

East Asian (EAS) AF: 0.684 AC: 3539 AN: 5172

South Asian (SAS) AF: 0.392 AC: 1893 AN: 4826

European-Finnish (FIN) AF: 0.469 AC: 4941 AN: 10540

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28981 AN: 67968

Other (OTH) AF: 0.458 AC: 965 AN: 2106

Alfa AF: 0.438 Hom.: 47636

Bravo AF: 0.493

Asia WGS AF: 0.536 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	13
DANN	Benign	0.65
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs770238; hg19: chr18-2527968;