rs2715368

Variant names:

• chr18-66081653-A-G
• rs2715368

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 0.485 in 151,830 control chromosomes in the GnomAD database, including 19,016 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 0.48 (19016 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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: 0.485 AC: 73508 AN: 151710 Hom.: 18982 Cov.: 31

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.485 AC: 73604 AN: 151830 Hom.: 19016 Cov.: 31 AF XY: 0.491 AC XY: 36416 AN XY: 74178

African (AFR) AF: 0.663 AC: 27461 AN: 41414

American (AMR) AF: 0.474 AC: 7230 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1702 AN: 3458

East Asian (EAS) AF: 0.539 AC: 2757 AN: 5114

South Asian (SAS) AF: 0.434 AC: 2090 AN: 4820

European-Finnish (FIN) AF: 0.489 AC: 5145 AN: 10512

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25725 AN: 67946

Other (OTH) AF: 0.482 AC: 1018 AN: 2114

Alfa AF: 0.416 Hom.: 43691

Bravo AF: 0.493

Asia WGS AF: 0.479 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.45
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs2715368; hg19: chr18-63748889;