rs1765267

Variant names:

• chr15-79580271-T-C
• rs1765267

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 0.0674 in 152,240 control chromosomes in the GnomAD database, including 619 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 0.067 (619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.578
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 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: 0.0672 AC: 10223 AN: 152122 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0452

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0278

Gnomad OTH AF: 0.0795

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

GnomAD4 genome AF: 0.0674 AC: 10259 AN: 152240 Hom.: 619 Cov.: 32 AF XY: 0.0711 AC XY: 5289 AN XY: 74438

African (AFR) AF: 0.104 AC: 4327 AN: 41554

American (AMR) AF: 0.0452 AC: 691 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0551 AC: 191 AN: 3468

East Asian (EAS) AF: 0.343 AC: 1772 AN: 5170

South Asian (SAS) AF: 0.109 AC: 526 AN: 4828

European-Finnish (FIN) AF: 0.0625 AC: 661 AN: 10582

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0278 AC: 1891 AN: 68018

Other (OTH) AF: 0.0858 AC: 181 AN: 2110

Alfa AF: 0.0426 Hom.: 137

Bravo AF: 0.0687

Asia WGS AF: 0.231 AC: 800 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.69
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1765267; hg19: chr15-79872613;