15-93198818-C-T

Variant names:

• chr15-93198818-C-T
• rs4777792
• ENST00000711606.1:n.616-13462C>T

Variant summary

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

The ENST00000711606.1(ENSG00000257060):​n.616-13462C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.749 in 152,134 control chromosomes in the GnomAD database, including 43,205 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 0.75 (43205 hom., cov: 32)
• Consequence: ENSG00000257060 ENST00000711606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.98
• Publications: 1 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257060	ENST00000711606.1	n.616-13462C>T		intron_variant	Intron 6 of 11
ENSG00000257060	ENST00000791023.1	n.312+28267C>T		intron_variant	Intron 3 of 6
ENSG00000257060	ENST00000791051.1	n.525+28267C>T		intron_variant	Intron 5 of 7
ENSG00000257060	ENST00000791055.1	n.462+28267C>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113928 AN: 152016 Hom.: 43167 Cov.: 32

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.749 AC: 114017 AN: 152134 Hom.: 43205 Cov.: 32 AF XY: 0.749 AC XY: 55679 AN XY: 74386

African (AFR) AF: 0.850 AC: 35311 AN: 41524

American (AMR) AF: 0.650 AC: 9930 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2101 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3849 AN: 5178

South Asian (SAS) AF: 0.683 AC: 3292 AN: 4818

European-Finnish (FIN) AF: 0.767 AC: 8106 AN: 10570

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.720 AC: 48936 AN: 67978

Other (OTH) AF: 0.719 AC: 1519 AN: 2112

Alfa AF: 0.721 Hom.: 6981

Bravo AF: 0.746

Asia WGS AF: 0.735 AC: 2555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.78
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs4777792; hg19: chr15-93742047;