rs2924572

chr15-47959841-T-Achr15-47959841-T-Cchr15-47959841-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657831.1(ENSG00000287439):n.713-11A>T variant causes a splice polypyrimidine tract, intron, non coding transcript 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: ENST00000657831.1 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298

Genes affected

LOC102724553 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC102724553	XR_001751520.2	n.1265A>T		non_coding_transcript_exon_variant	3/3
LOC124900354	XR_001751516.3	n.143-32868T>A		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751517.2	n.143-32868T>A		intron_variant, non_coding_transcript_variant
LOC124900354	XR_001751518.3	n.83-32868T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657831.1	n.713-11A>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant
	ENST00000662551.1	n.189-32868T>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.971

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.976

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.919

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2924572; hg19: chr15-48252038;