rs1471169

Variant names:

• chr15-95119290-G-A
• rs1471169
• ENST00000554787.1:n.266+13304C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-95119290-G-A
• chr15-95119290-G-C
• chr15-95119290-G-T

Variant summary

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

The ENST00000554787.1(ENSG00000258773):​n.266+13304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 151,926 control chromosomes in the GnomAD database, including 34,887 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 0.68 (34887 hom., cov: 32)
• Consequence: ENSG00000258773 ENST00000554787.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.39
• 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=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370991	XR_002957693.2	n.488-3635G>A		intron_variant	Intron 4 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258773	ENST00000554787.1	n.266+13304C>T		intron_variant	Intron 1 of 2	4
ENSG00000293024	ENST00000615751.5	n.491-3635G>A		intron_variant	Intron 4 of 6	5
ENSG00000293024	ENST00000616940.1	n.146-3635G>A		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102618 AN: 151806 Hom.: 34857 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.676 AC: 102696 AN: 151926 Hom.: 34887 Cov.: 32 AF XY: 0.675 AC XY: 50087 AN XY: 74246

African (AFR) AF: 0.632 AC: 26189 AN: 41442

American (AMR) AF: 0.695 AC: 10590 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2700 AN: 3464

East Asian (EAS) AF: 0.596 AC: 3059 AN: 5136

South Asian (SAS) AF: 0.689 AC: 3313 AN: 4810

European-Finnish (FIN) AF: 0.666 AC: 7028 AN: 10558

Middle Eastern (MID) AF: 0.815 AC: 238 AN: 292

European-Non Finnish (NFE) AF: 0.698 AC: 47428 AN: 67960

Other (OTH) AF: 0.688 AC: 1451 AN: 2108

Alfa AF: 0.698 Hom.: 158626

Bravo AF: 0.674

Asia WGS AF: 0.691 AC: 2404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	11
DANN	Benign	0.46
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs1471169; hg19: chr15-95662519;