rs1520961

Variant names:

• chr15-37444454-G-A
• rs1520961
• ENST00000561054.2:n.89-17692C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000561054.2(ENSG00000259434):​n.89-17692C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,856 control chromosomes in the GnomAD database, including 4,968 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 0.25 (4968 hom., cov: 32)
• Consequence: ENSG00000259434 ENST00000561054.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808
• Publications: 2 publications found

Genes affected

ENSG00000259434 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 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
ENSG00000259434	ENST00000561054.2	n.89-17692C>T		intron_variant	Intron 1 of 4	3
ENSG00000259434	ENST00000663330.1	n.116-24269C>T		intron_variant	Intron 1 of 3
ENSG00000259434	ENST00000669587.1	n.127-24269C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37915 AN: 151736 Hom.: 4973 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.368

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.250 AC: 37916 AN: 151856 Hom.: 4968 Cov.: 32 AF XY: 0.247 AC XY: 18303 AN XY: 74228

African (AFR) AF: 0.200 AC: 8296 AN: 41424

American (AMR) AF: 0.243 AC: 3695 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1347 AN: 3468

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5182

South Asian (SAS) AF: 0.299 AC: 1439 AN: 4820

European-Finnish (FIN) AF: 0.197 AC: 2084 AN: 10552

Middle Eastern (MID) AF: 0.355 AC: 103 AN: 290

European-Non Finnish (NFE) AF: 0.295 AC: 20020 AN: 67868

Other (OTH) AF: 0.270 AC: 568 AN: 2106

Alfa AF: 0.272 Hom.: 795

Bravo AF: 0.248

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.55
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1520961; hg19: chr15-37736655;