rs1258824

Variant names:

• chr15-95100167-T-A
• rs291038
• ENST00000554787.1:n.267-7897A>T

Your query was ambiguous. Multiple possible variants found:

• chr15-95100167-T-A
• chr15-95100167-T-C

Variant summary

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

The ENST00000554787.1(ENSG00000258773):​n.267-7897A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,892 control chromosomes in the GnomAD database, including 4,803 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 0.24 (4803 hom., cov: 31)
• Consequence: ENSG00000258773 ENST00000554787.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 0 publications found

Genes affected

ENSG00000258773 (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 (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370991	XR_002957693.2	n.488-22758T>A		intron_variant	Intron 4 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258773	ENST00000554787.1	n.267-7897A>T		intron_variant	Intron 1 of 2	4
ENSG00000293024	ENST00000615751.5	n.491-22758T>A		intron_variant	Intron 4 of 6	5
ENSG00000293024	ENST00000616940.1	n.146-22758T>A		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36385 AN: 151772 Hom.: 4792 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.240 AC: 36407 AN: 151892 Hom.: 4803 Cov.: 31 AF XY: 0.244 AC XY: 18153 AN XY: 74292

African (AFR) AF: 0.134 AC: 5560 AN: 41428

American (AMR) AF: 0.260 AC: 3965 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2001 AN: 5152

South Asian (SAS) AF: 0.292 AC: 1409 AN: 4822

European-Finnish (FIN) AF: 0.307 AC: 3231 AN: 10510

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18842 AN: 67926

Other (OTH) AF: 0.245 AC: 515 AN: 2106

Alfa AF: 0.138 Hom.: 284

Bravo AF: 0.233

Asia WGS AF: 0.296 AC: 1026 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.63
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs291038; hg19: chr15-95643396;