rs1554865

Variant names:

• chr15-32707605-C-T
• rs1554865

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 0.67 in 151,924 control chromosomes in the GnomAD database, including 36,180 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 0.67 (36180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.789 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: 0.670 AC: 101647 AN: 151806 Hom.: 36157 Cov.: 31

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.670 AC: 101716 AN: 151924 Hom.: 36180 Cov.: 31 AF XY: 0.665 AC XY: 49376 AN XY: 74250

African (AFR) AF: 0.467 AC: 19312 AN: 41340

American (AMR) AF: 0.731 AC: 11165 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2983 AN: 3470

East Asian (EAS) AF: 0.243 AC: 1256 AN: 5172

South Asian (SAS) AF: 0.597 AC: 2867 AN: 4806

European-Finnish (FIN) AF: 0.713 AC: 7521 AN: 10542

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54065 AN: 68004

Other (OTH) AF: 0.708 AC: 1493 AN: 2108

Alfa AF: 0.768 Hom.: 19753

Bravo AF: 0.664

Asia WGS AF: 0.429 AC: 1494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1554865; hg19: chr15-32999806;