chr15-47976289-G-T

Variant names:

• chr15-47976289-G-T
• rs2924567
• ENST00000560900.1:n.196-16420G>T

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.196-16420G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 152,038 control chromosomes in the GnomAD database, including 6,209 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 0.25 (6209 hom., cov: 31)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674
• Publications: 4 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.143-16420G>T		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.143-16420G>T		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.83-16420G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.196-16420G>T		intron_variant	Intron 1 of 2	4
ENSG00000287439	ENST00000657831.2	n.441+11348C>A		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000662551.1	n.189-16420G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38207 AN: 151920 Hom.: 6216 Cov.: 31

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.251 AC: 38188 AN: 152038 Hom.: 6209 Cov.: 31 AF XY: 0.248 AC XY: 18422 AN XY: 74306

African (AFR) AF: 0.0691 AC: 2868 AN: 41482

American (AMR) AF: 0.273 AC: 4166 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1346 AN: 3470

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5172

South Asian (SAS) AF: 0.258 AC: 1243 AN: 4816

European-Finnish (FIN) AF: 0.279 AC: 2948 AN: 10568

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24524 AN: 67950

Other (OTH) AF: 0.291 AC: 615 AN: 2110

Alfa AF: 0.282 Hom.: 1184

Bravo AF: 0.242

Asia WGS AF: 0.108 AC: 374 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.43
DANN	Benign	0.35
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2924567; hg19: chr15-48268486;