ENST00000561054.2:n.313+2108T>C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370772	XR_932115.3	n.220+2108T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259434	ENST00000561054.2	n.313+2108T>C		intron_variant	Intron 3 of 4	3
ENSG00000259434	ENST00000663330.1	n.241+2108T>C		intron_variant	Intron 2 of 3
ENSG00000259434	ENST00000669587.1	n.387+1488T>C		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs1520954; hg19: chr15-37710153;