chr15-98144101-T-C

Variant names:

• chr15-98144101-T-C
• rs12437601
• ENST00000560360.2:n.314-97362A>G

Variant summary

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

The ENST00000560360.2(ENSG00000259199):​n.314-97362A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0639 in 152,010 control chromosomes in the GnomAD database, including 411 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 0.064 (411 hom., cov: 31)
• Consequence: ENSG00000259199 ENST00000560360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

Genes affected

ENSG00000259199 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0808 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.314-97362A>G		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0640 AC: 9714 AN: 151890 Hom.: 412 Cov.: 31

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0736

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.0380

Gnomad SAS AF: 0.0823

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0826

Gnomad OTH AF: 0.0551

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

GnomAD4 genome AF: 0.0639 AC: 9710 AN: 152010 Hom.: 411 Cov.: 31 AF XY: 0.0661 AC XY: 4911 AN XY: 74308

Gnomad4 AFR AF: 0.0148

Gnomad4 AMR AF: 0.0736

Gnomad4 ASJ AF: 0.0392

Gnomad4 EAS AF: 0.0375

Gnomad4 SAS AF: 0.0825

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0826

Gnomad4 OTH AF: 0.0546

Alfa AF: 0.0763 Hom.: 646

Bravo AF: 0.0551

Asia WGS AF: 0.0520 AC: 179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.57
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12437601; hg19: chr15-98687330;