chr15-90855370-C-T

Variant names:

• chr15-90855370-C-T
• rs34050628
• ENST00000723685.1:n.368-260C>T

Variant summary

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

The ENST00000723685.1(ENSG00000259704):​n.368-260C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.086 in 152,266 control chromosomes in the GnomAD database, including 761 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 0.086 (761 hom., cov: 32)
• Consequence: ENSG00000259704 ENST00000723685.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 2 publications found

Genes affected

ENSG00000259704 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723685.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259704	ENST00000723685.1		n.368-260C>T		intron	N/A
	ENSG00000259704	ENST00000723686.1		n.198-260C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13093 AN: 152148 Hom.: 759 Cov.: 32

Gnomad AFR AF: 0.0236

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0860 AC: 13089 AN: 152266 Hom.: 761 Cov.: 32 AF XY: 0.0862 AC XY: 6422 AN XY: 74460

African (AFR) AF: 0.0236 AC: 980 AN: 41570

American (AMR) AF: 0.0757 AC: 1158 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 558 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5186

South Asian (SAS) AF: 0.141 AC: 679 AN: 4816

European-Finnish (FIN) AF: 0.118 AC: 1254 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8142 AN: 67992

Other (OTH) AF: 0.106 AC: 225 AN: 2114

Alfa AF: 0.0754 Hom.: 235

Bravo AF: 0.0787

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.95
DANN	Benign	0.80
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs34050628; hg19: chr15-91398600;