rs16960516

Variant names:

• chr15-48037345-A-G
• rs16960516
• ENST00000560900.1:n.259-11445A>G

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.259-11445A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 152,292 control chromosomes in the GnomAD database, including 348 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 0.056 (348 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• Publications: 0 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.206-11445A>G		intron_variant	Intron 2 of 2
LOC124900354	XR_001751518.3	n.146-11445A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.259-11445A>G		intron_variant	Intron 2 of 2	4
ENSG00000259754	ENST00000662551.1	n.252-11445A>G		intron_variant	Intron 2 of 2
ENSG00000259754	ENST00000665188.1	n.221-11492A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8566 AN: 152174 Hom.: 350 Cov.: 32

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0348

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.00539

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0562 AC: 8562 AN: 152292 Hom.: 348 Cov.: 32 AF XY: 0.0588 AC XY: 4381 AN XY: 74460

African (AFR) AF: 0.0136 AC: 566 AN: 41580

American (AMR) AF: 0.0348 AC: 532 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0992 AC: 344 AN: 3468

East Asian (EAS) AF: 0.00540 AC: 28 AN: 5186

South Asian (SAS) AF: 0.150 AC: 723 AN: 4828

European-Finnish (FIN) AF: 0.108 AC: 1145 AN: 10602

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0745 AC: 5067 AN: 68014

Other (OTH) AF: 0.0421 AC: 89 AN: 2114

Alfa AF: 0.0608 Hom.: 138

Bravo AF: 0.0469

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.99
DANN	Benign	0.55
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs16960516; hg19: chr15-48329542;