15-47990939-C-G

Variant names:

• chr15-47990939-C-G
• rs16960453
• ENST00000560900.1:n.196-1770C>G

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.196-1770C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0705 in 152,186 control chromosomes in the GnomAD database, including 1,027 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 0.070 (1027 hom., cov: 32)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.375
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.143-1770C>G		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.143-1770C>G		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.83-1770C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.196-1770C>G		intron_variant	Intron 1 of 2	4
ENSG00000259754	ENST00000662551.1	n.189-1770C>G		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.189-1770C>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0703 AC: 10683 AN: 152068 Hom.: 1021 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00501

Gnomad SAS AF: 0.0944

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000735

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0705 AC: 10728 AN: 152186 Hom.: 1027 Cov.: 32 AF XY: 0.0693 AC XY: 5158 AN XY: 74402

African (AFR) AF: 0.209 AC: 8655 AN: 41478

American (AMR) AF: 0.0940 AC: 1436 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00502 AC: 26 AN: 5178

South Asian (SAS) AF: 0.0934 AC: 450 AN: 4816

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.000735 AC: 50 AN: 68028

Other (OTH) AF: 0.0501 AC: 106 AN: 2114

Alfa AF: 0.00255 Hom.: 2

Bravo AF: 0.0839

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.7
DANN	Benign	0.54
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs16960453; hg19: chr15-48283136;