rs873393

chr15-57883080-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 0.502 in 152,066 control chromosomes in the GnomAD database, including 20,736 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 0.50 (20736 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944

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 (NFE) allele frequency at 95% confidence interval = 0.614 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: 0.503 AC: 76354 AN: 151948 Hom.: 20727 Cov.: 31

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.502 AC: 76384 AN: 152066 Hom.: 20736 Cov.: 31 AF XY: 0.497 AC XY: 36963 AN XY: 74322

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.619

Gnomad4 OTH AF: 0.532

Alfa AF: 0.602 Hom.: 56018

Bravo AF: 0.496

Asia WGS AF: 0.477 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.39
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs873393; hg19: chr15-58175278;