rs2924572

Variant names:

• chr15-47959841-T-A
• rs2924572
• XR_001751520.2:n.1265A>T

Your query was ambiguous. Multiple possible variants found:

• chr15-47959841-T-A
• chr15-47959841-T-C
• chr15-47959841-T-G

Variant summary

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

The XR_001751520.2(LOC102724553):​n.1265A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,014 control chromosomes in the GnomAD database, including 62,687 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 0.90 (62687 hom., cov: 30)
• Consequence: LOC102724553 XR_001751520.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 0 publications found

Genes affected

LOC102724553 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724553	XR_001751520.2	n.1265A>T		non_coding_transcript_exon_variant	Exon 3 of 3
LOC124900354	XR_001751516.3	n.143-32868T>A		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.143-32868T>A		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.83-32868T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.196-32868T>A		intron_variant	Intron 1 of 2	4
ENSG00000287439	ENST00000657831.2	n.746-11A>T		intron_variant	Intron 2 of 2
ENSG00000259754	ENST00000662551.1	n.189-32868T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137406 AN: 151896 Hom.: 62667 Cov.: 30

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.971

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.904 AC: 137476 AN: 152014 Hom.: 62687 Cov.: 30 AF XY: 0.903 AC XY: 67102 AN XY: 74292

African (AFR) AF: 0.804 AC: 33284 AN: 41416

American (AMR) AF: 0.861 AC: 13146 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.971 AC: 3373 AN: 3472

East Asian (EAS) AF: 0.772 AC: 3963 AN: 5136

South Asian (SAS) AF: 0.871 AC: 4192 AN: 4812

European-Finnish (FIN) AF: 0.976 AC: 10345 AN: 10596

Middle Eastern (MID) AF: 0.979 AC: 286 AN: 292

European-Non Finnish (NFE) AF: 0.972 AC: 66083 AN: 68010

Other (OTH) AF: 0.919 AC: 1936 AN: 2106

Alfa AF: 0.945 Hom.: 7946

Bravo AF: 0.890

Asia WGS AF: 0.825 AC: 2867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.4
DANN	Benign	0.77
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2924572; hg19: chr15-48252038;