rs2615787

Variant names:

• chr8-6953627-T-G
• rs2615787

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 0.408 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.411 AC: 17053 AN: 41528

American (AMR) AF: 0.370 AC: 5661 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1500 AN: 3464

East Asian (EAS) AF: 0.344 AC: 1778 AN: 5170

South Asian (SAS) AF: 0.380 AC: 1834 AN: 4826

European-Finnish (FIN) AF: 0.437 AC: 4616 AN: 10558

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28325 AN: 67962

Other (OTH) AF: 0.404 AC: 853 AN: 2114

Alfa AF: 0.427 Hom.: 4838

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs2615787; hg19: chr8-6811149;