chr15-57355814-T-C

Variant names:

• chr15-57355814-T-C
• rs734489

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 0.628 in 152,106 control chromosomes in the GnomAD database, including 30,151 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 0.63 (30151 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.770
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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: 0.628 AC: 95482 AN: 151988 Hom.: 30136 Cov.: 33

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.628 AC: 95548 AN: 152106 Hom.: 30151 Cov.: 33 AF XY: 0.629 AC XY: 46776 AN XY: 74346

African (AFR) AF: 0.648 AC: 26883 AN: 41478

American (AMR) AF: 0.609 AC: 9311 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1813 AN: 3470

East Asian (EAS) AF: 0.675 AC: 3488 AN: 5170

South Asian (SAS) AF: 0.623 AC: 3006 AN: 4826

European-Finnish (FIN) AF: 0.656 AC: 6946 AN: 10584

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42096 AN: 67974

Other (OTH) AF: 0.628 AC: 1327 AN: 2114

Alfa AF: 0.617 Hom.: 94459

Bravo AF: 0.625

Asia WGS AF: 0.628 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.40
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs734489; hg19: chr15-57648012;