ENST00000561123.3:n.748-2679C>T

Variant names:

• chr15-77605861-C-T
• rs4886887
• ENST00000561123.3:n.748-2679C>T

Variant summary

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

The ENST00000561123.3(ENSG00000259420):​n.748-2679C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,156 control chromosomes in the GnomAD database, including 3,600 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 0.21 (3600 hom., cov: 33)
• Consequence: ENSG00000259420 ENST00000561123.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 4 publications found

Genes affected

ENSG00000259420 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370906	XR_001751806.2	n.689-24424C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259420	ENST00000561123.3	n.748-2679C>T		intron_variant	Intron 3 of 3	3
ENSG00000259420	ENST00000725807.1	n.564-2679C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32209 AN: 152038 Hom.: 3602 Cov.: 33

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.212 AC: 32206 AN: 152156 Hom.: 3600 Cov.: 33 AF XY: 0.208 AC XY: 15489 AN XY: 74392

African (AFR) AF: 0.148 AC: 6162 AN: 41516

American (AMR) AF: 0.239 AC: 3656 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3472

East Asian (EAS) AF: 0.189 AC: 976 AN: 5158

South Asian (SAS) AF: 0.193 AC: 934 AN: 4828

European-Finnish (FIN) AF: 0.204 AC: 2164 AN: 10600

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16946 AN: 67966

Other (OTH) AF: 0.217 AC: 460 AN: 2116

Alfa AF: 0.228 Hom.: 538

Bravo AF: 0.212

Asia WGS AF: 0.179 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.39
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs4886887; hg19: chr15-77898203;