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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554787.1. 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
	ENSG00000258773	ENST00000554787.1	TSL:4	n.267-7897A>T		intron	N/A
	ENSG00000293024	ENST00000615751.5	TSL:5	n.491-22758T>A		intron	N/A
	ENSG00000293024	ENST00000616940.1	TSL:5	n.146-22758T>A		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs291038;

hg19: chr15-95643396;