chr15-47982650-A-G

Variant names:

• chr15-47982650-A-G
• rs16960438
• ENST00000560900.1:n.196-10059A>G

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.196-10059A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0417 in 152,210 control chromosomes in the GnomAD database, including 269 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 0.042 (269 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.143-10059A>G		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.143-10059A>G		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.83-10059A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.196-10059A>G		intron_variant	Intron 1 of 2	4
ENSG00000287439	ENST00000657831.2	n.441+4987T>C		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000662551.1	n.189-10059A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0416 AC: 6333 AN: 152092 Hom.: 270 Cov.: 32

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0311

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.0770

Gnomad FIN AF: 0.0339

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0360

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

GnomAD4 genome AF: 0.0417 AC: 6343 AN: 152210 Hom.: 269 Cov.: 32 AF XY: 0.0441 AC XY: 3283 AN XY: 74430

African (AFR) AF: 0.0830 AC: 3448 AN: 41522

American (AMR) AF: 0.0312 AC: 477 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0254 AC: 88 AN: 3468

East Asian (EAS) AF: 0.160 AC: 826 AN: 5168

South Asian (SAS) AF: 0.0771 AC: 371 AN: 4814

European-Finnish (FIN) AF: 0.0339 AC: 360 AN: 10614

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 684 AN: 68028

Other (OTH) AF: 0.0370 AC: 78 AN: 2108

Alfa AF: 0.0223 Hom.: 14

Bravo AF: 0.0438

Asia WGS AF: 0.129 AC: 445 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.75
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs16960438; hg19: chr15-48274847;