rs524952

Variant names:

• chr15-34713685-T-A
• rs524952
• ENST00000720751.1:n.234+6632A>T

Your query was ambiguous. Multiple possible variants found:

• chr15-34713685-T-A
• chr15-34713685-T-C

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.234+6632A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,108 control chromosomes in the GnomAD database, including 19,181 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 0.50 (19181 hom., cov: 32)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324
• Publications: 51 publications found

Genes affected

ENSG00000294065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 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
ENSG00000294065	ENST00000720751.1	n.234+6632A>T		intron_variant	Intron 1 of 1
ENSG00000294065	ENST00000720752.1	n.187+6632A>T		intron_variant	Intron 1 of 1
ENSG00000294065	ENST00000720753.1	n.550-2857A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75643 AN: 151990 Hom.: 19169 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.498 AC: 75691 AN: 152108 Hom.: 19181 Cov.: 32 AF XY: 0.491 AC XY: 36539 AN XY: 74382

African (AFR) AF: 0.575 AC: 23830 AN: 41474

American (AMR) AF: 0.462 AC: 7063 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1428 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2336 AN: 5180

South Asian (SAS) AF: 0.615 AC: 2966 AN: 4820

European-Finnish (FIN) AF: 0.342 AC: 3620 AN: 10584

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32608 AN: 67974

Other (OTH) AF: 0.492 AC: 1040 AN: 2114

Alfa AF: 0.486 Hom.: 2245

Bravo AF: 0.506

Asia WGS AF: 0.530 AC: 1845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.19
DANN	Benign	0.62
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs524952; hg19: chr15-35005886;