15-70296933-T-C

Variant names:

• chr15-70296933-T-C
• rs12148337
• ENST00000819859.1:n.631-20948A>G

Variant summary

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

The ENST00000819859.1(ENSG00000306630):​n.631-20948A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 150,836 control chromosomes in the GnomAD database, including 17,084 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 0.47 (17084 hom., cov: 32)
• Consequence: ENSG00000306630 ENST00000819859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.362
• Publications: 27 publications found

Genes affected

ENSG00000306630 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819859.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306630	ENST00000819859.1		n.631-20948A>G		intron	N/A
	ENSG00000306630	ENST00000819860.1		n.173-610A>G		intron	N/A
	ENSG00000306630	ENST00000819861.1		n.415-610A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70159 AN: 150722 Hom.: 17078 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.465 AC: 70174 AN: 150836 Hom.: 17084 Cov.: 32 AF XY: 0.467 AC XY: 34399 AN XY: 73634

African (AFR) AF: 0.304 AC: 12368 AN: 40732

American (AMR) AF: 0.482 AC: 7291 AN: 15126

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1569 AN: 3460

East Asian (EAS) AF: 0.485 AC: 2473 AN: 5096

South Asian (SAS) AF: 0.476 AC: 2258 AN: 4744

European-Finnish (FIN) AF: 0.566 AC: 5944 AN: 10510

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36593 AN: 67886

Other (OTH) AF: 0.464 AC: 967 AN: 2086

Alfa AF: 0.523 Hom.: 25263

Bravo AF: 0.448

Asia WGS AF: 0.423 AC: 1472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.74
PhyloP100		0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12148337;

hg19: chr15-70589272;