rs1520954

Variant names:

• chr15-37417952-A-G
• rs1520954
• ENST00000561054.2:n.313+2108T>C

Variant summary

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

The ENST00000561054.2(ENSG00000259434):​n.313+2108T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,996 control chromosomes in the GnomAD database, including 18,286 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 0.48 (18286 hom., cov: 32)
• Consequence: ENSG00000259434 ENST00000561054.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561054.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259434	ENST00000561054.2	TSL:3	n.313+2108T>C		intron	N/A
	ENSG00000259434	ENST00000663330.1		n.241+2108T>C		intron	N/A
	ENSG00000259434	ENST00000669587.1		n.387+1488T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73638 AN: 151878 Hom.: 18266 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.485 AC: 73699 AN: 151996 Hom.: 18286 Cov.: 32 AF XY: 0.474 AC XY: 35246 AN XY: 74292

African (AFR) AF: 0.451 AC: 18704 AN: 41456

American (AMR) AF: 0.516 AC: 7874 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2158 AN: 3464

East Asian (EAS) AF: 0.193 AC: 998 AN: 5168

South Asian (SAS) AF: 0.397 AC: 1915 AN: 4824

European-Finnish (FIN) AF: 0.363 AC: 3833 AN: 10566

Middle Eastern (MID) AF: 0.658 AC: 192 AN: 292

European-Non Finnish (NFE) AF: 0.536 AC: 36415 AN: 67952

Other (OTH) AF: 0.519 AC: 1096 AN: 2110

Alfa AF: 0.520 Hom.: 9607

Bravo AF: 0.499

Asia WGS AF: 0.319 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.36
DANN	Benign	0.23
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1520954;

hg19: chr15-37710153;