rs4965458

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-98135295-C-A
• chr15-98135295-C-G
• chr15-98135295-C-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000259199 (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 (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
ENSG00000259199	ENST00000717124.1	n.292-88556G>T		intron_variant	Intron 3 of 8

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

African (AFR) AF: 0.949 AC: 39460 AN: 41574

American (AMR) AF: 0.909 AC: 13897 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3218 AN: 3472

East Asian (EAS) AF: 0.932 AC: 4814 AN: 5166

South Asian (SAS) AF: 0.901 AC: 4347 AN: 4824

European-Finnish (FIN) AF: 0.850 AC: 9021 AN: 10616

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56521 AN: 68026

Other (OTH) AF: 0.883 AC: 1864 AN: 2112

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
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs4965458; hg19: chr15-98678524;