chr15-96062683-C-T

Variant names:

• chr15-96062683-C-T
• rs11636705
• ENST00000558860.2:n.81+1594G>A

Variant summary

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

The ENST00000558860.2(ENSG00000259702):​n.81+1594G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,058 control chromosomes in the GnomAD database, including 2,019 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 0.16 (2019 hom., cov: 32)
• Consequence: ENSG00000259702 ENST00000558860.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 1 publications found

Genes affected

ENSG00000259702 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268156	XR_002957737.1	n.450+71799C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259702	ENST00000558860.2	n.81+1594G>A		intron_variant	Intron 1 of 3	4
ENSG00000275443	ENST00000619812.1	n.303+71799C>T		intron_variant	Intron 1 of 3	5
ENSG00000259702	ENST00000648034.2	n.217+1G>A		splice_donor_variant, intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24250 AN: 151942 Hom.: 2015 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.160 AC: 24264 AN: 152058 Hom.: 2019 Cov.: 32 AF XY: 0.162 AC XY: 12027 AN XY: 74332

African (AFR) AF: 0.150 AC: 6230 AN: 41480

American (AMR) AF: 0.161 AC: 2462 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3470

East Asian (EAS) AF: 0.103 AC: 535 AN: 5170

South Asian (SAS) AF: 0.211 AC: 1017 AN: 4822

European-Finnish (FIN) AF: 0.195 AC: 2060 AN: 10546

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10963 AN: 67974

Other (OTH) AF: 0.145 AC: 307 AN: 2110

Alfa AF: 0.105 Hom.: 240

Bravo AF: 0.154

Asia WGS AF: 0.169 AC: 587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.46
DANN	Benign	0.73
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11636705; hg19: chr15-96605912;