ENST00000560900.1:n.196-25187T>C

Variant names:

• chr15-47967522-T-C
• rs2934193
• ENST00000560900.1:n.196-25187T>C

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.196-25187T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 151,996 control chromosomes in the GnomAD database, including 31,038 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 0.57 (31038 hom., cov: 31)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.143-25187T>C		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.143-25187T>C		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.83-25187T>C		intron_variant	Intron 1 of 2
LOC102724553	XR_001751520.2	n.481-6897A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.196-25187T>C		intron_variant	Intron 1 of 2	4
ENSG00000287439	ENST00000657831.2	n.442-6897A>G		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000662551.1	n.189-25187T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86729 AN: 151878 Hom.: 31050 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.570 AC: 86709 AN: 151996 Hom.: 31038 Cov.: 31 AF XY: 0.571 AC XY: 42376 AN XY: 74268

African (AFR) AF: 0.162 AC: 6727 AN: 41458

American (AMR) AF: 0.557 AC: 8486 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2666 AN: 3472

East Asian (EAS) AF: 0.174 AC: 901 AN: 5172

South Asian (SAS) AF: 0.627 AC: 3010 AN: 4800

European-Finnish (FIN) AF: 0.782 AC: 8278 AN: 10582

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54436 AN: 67958

Other (OTH) AF: 0.600 AC: 1262 AN: 2104

Alfa AF: 0.738 Hom.: 22141

Bravo AF: 0.530

Asia WGS AF: 0.351 AC: 1223 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	1.4
DANN	Benign	0.67
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2934193; hg19: chr15-48259719;