rs16960493

Variant names:

• chr15-48017250-T-G
• rs16960493
• ENST00000560900.1:n.258+24479T>G

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.258+24479T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,172 control chromosomes in the GnomAD database, including 5,285 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 0.17 (5285 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.205+24479T>G		intron_variant	Intron 2 of 2
LOC124900354	XR_001751518.3	n.145+24479T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.258+24479T>G		intron_variant	Intron 2 of 2	4
ENSG00000259754	ENST00000662551.1	n.251+24479T>G		intron_variant	Intron 2 of 2
ENSG00000259754	ENST00000665188.1	n.220+19095T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26326 AN: 152056 Hom.: 5270 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.00951

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.0229

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0268

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.173 AC: 26388 AN: 152172 Hom.: 5285 Cov.: 32 AF XY: 0.170 AC XY: 12656 AN XY: 74402

African (AFR) AF: 0.469 AC: 19461 AN: 41472

American (AMR) AF: 0.144 AC: 2195 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00951 AC: 33 AN: 3470

East Asian (EAS) AF: 0.373 AC: 1927 AN: 5162

South Asian (SAS) AF: 0.0807 AC: 389 AN: 4820

European-Finnish (FIN) AF: 0.0229 AC: 243 AN: 10622

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0268 AC: 1822 AN: 68012

Other (OTH) AF: 0.135 AC: 285 AN: 2116

Alfa AF: 0.0749 Hom.: 2281

Bravo AF: 0.200

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.43
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs16960493; hg19: chr15-48309447;