rs2615787

Variant names:

• chr8-6953627-T-G
• rs2615787

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 0.408 in 152,110 control chromosomes in the GnomAD database, including 12,754 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 0.41 (12754 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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: 0.408 AC: 61964 AN: 151992 Hom.: 12725 Cov.: 33

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.408 AC: 62046 AN: 152110 Hom.: 12754 Cov.: 33 AF XY: 0.408 AC XY: 30322 AN XY: 74344

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.437

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.404

Alfa AF: 0.410 Hom.: 3033

Bravo AF: 0.401

Asia WGS AF: 0.416 AC: 1447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2615787; hg19: chr8-6811149;