rs873393

Variant names:

• chr15-57883080-T-C
• rs873393

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 0.502 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.300 AC: 12433 AN: 41490

American (AMR) AF: 0.569 AC: 8702 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2097 AN: 3470

East Asian (EAS) AF: 0.290 AC: 1497 AN: 5166

South Asian (SAS) AF: 0.569 AC: 2742 AN: 4820

European-Finnish (FIN) AF: 0.469 AC: 4953 AN: 10566

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42046 AN: 67958

Other (OTH) AF: 0.532 AC: 1121 AN: 2108

Alfa AF: 0.588 Hom.: 76602

Bravo AF: 0.496

Asia WGS AF: 0.477 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.64
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs873393; hg19: chr15-58175278;