rs12437601

Positions:

• chr15-98144101-T-C

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, non coding transcript 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: ENST00000560360.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000560360.2	n.314-97362A>G		intron_variant, non_coding_transcript_variant		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;