rs2715368

Variant names:

• chr18-66081653-A-G
• rs2715368

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 0.485 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.482

Alfa AF: 0.400 Hom.: 25269

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2715368; hg19: chr18-63748889;