rs770238

Positions:

• chr18-2527969-C-A

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 0.491 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.458

Alfa AF: 0.422 Hom.: 27747

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs770238; hg19: chr18-2527968;