rs692153

chr15-41160483-G-A

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 0.488 in 151,802 control chromosomes in the GnomAD database, including 19,178 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 0.49 (19178 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73938 AN: 151686 Hom.: 19126 Cov.: 30

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.488 AC: 74047 AN: 151802 Hom.: 19178 Cov.: 30 AF XY: 0.483 AC XY: 35827 AN XY: 74158

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.472

Alfa AF: 0.478 Hom.: 4151

Bravo AF: 0.494

Asia WGS AF: 0.450 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.0
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs692153; hg19: chr15-41452681;