chr15-98135295-C-A

Variant names:

• chr15-98135295-C-A
• rs4965458
• ENST00000560360.2:n.314-88556G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560360.2(ENSG00000259199):​n.314-88556G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.881 in 152,288 control chromosomes in the GnomAD database, including 59,344 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 0.88 (59344 hom., cov: 34)
• Consequence: ENSG00000259199 ENST00000560360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

Genes affected

ENSG00000259199 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 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
ENSG00000259199	ENST00000560360.2	n.314-88556G>T		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.881 AC: 134040 AN: 152170 Hom.: 59276 Cov.: 34

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.881 AC: 134166 AN: 152288 Hom.: 59344 Cov.: 34 AF XY: 0.883 AC XY: 65757 AN XY: 74454

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.909

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.850

Gnomad4 NFE AF: 0.831

Gnomad4 OTH AF: 0.883

Alfa AF: 0.861 Hom.: 10813

Bravo AF: 0.889

Asia WGS AF: 0.941 AC: 3272 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	0.36
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4965458; hg19: chr15-98678524;