15-99564180-C-T

Variant names:

• chr15-99564180-C-T
• rs4424892
• ENST00000848429.1:n.115-34G>A

Variant summary

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

The ENST00000848429.1(ENSG00000310223):​n.115-34G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,058 control chromosomes in the GnomAD database, including 44,990 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 0.76 (44990 hom., cov: 31)
• Consequence: ENSG00000310223 ENST00000848429.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 4 publications found

Genes affected

ENSG00000310223 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.839 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
ENSG00000310223	ENST00000848429.1	n.115-34G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116204 AN: 151940 Hom.: 44955 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.765 AC: 116293 AN: 152058 Hom.: 44990 Cov.: 31 AF XY: 0.769 AC XY: 57177 AN XY: 74340

African (AFR) AF: 0.662 AC: 27419 AN: 41444

American (AMR) AF: 0.728 AC: 11123 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2972 AN: 3472

East Asian (EAS) AF: 0.735 AC: 3799 AN: 5172

South Asian (SAS) AF: 0.861 AC: 4142 AN: 4812

European-Finnish (FIN) AF: 0.873 AC: 9244 AN: 10594

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54840 AN: 67984

Other (OTH) AF: 0.786 AC: 1652 AN: 2102

Alfa AF: 0.774 Hom.: 7518

Bravo AF: 0.749

Asia WGS AF: 0.794 AC: 2758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4424892; hg19: chr15-100104385;