rs1765267

Positions:

• chr15-79580271-T-C

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 0.0674 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0452

Gnomad4 ASJ AF: 0.0551

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0625

Gnomad4 NFE AF: 0.0278

Gnomad4 OTH AF: 0.0858

Alfa AF: 0.0423 Hom.: 96

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1765267; hg19: chr15-79872613;