15-67861394-G-C

Variant names:

• chr15-67861394-G-C
• rs16951358
• ENST00000558889.5:n.122-12303G>C

Variant summary

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

The ENST00000812769.1(ENSG00000259410):​n.262-12303G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,912 control chromosomes in the GnomAD database, including 8,639 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 0.32 (8639 hom., cov: 31)
• Consequence: ENSG00000259410 ENST00000812769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590
• Publications: 1 publications found

Genes affected

ENSG00000259410 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812769.1. 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
	ENSG00000259410	ENST00000558889.5	TSL:5	n.122-12303G>C		intron	N/A
	ENSG00000259410	ENST00000560577.1	TSL:5	n.177-12303G>C		intron	N/A
	ENSG00000259410	ENST00000812769.1		n.262-12303G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48875 AN: 151794 Hom.: 8615 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.322 AC: 48942 AN: 151912 Hom.: 8639 Cov.: 31 AF XY: 0.325 AC XY: 24158 AN XY: 74242

African (AFR) AF: 0.318 AC: 13153 AN: 41382

American (AMR) AF: 0.412 AC: 6300 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1326 AN: 3466

East Asian (EAS) AF: 0.744 AC: 3824 AN: 5140

South Asian (SAS) AF: 0.448 AC: 2159 AN: 4814

European-Finnish (FIN) AF: 0.226 AC: 2382 AN: 10544

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18808 AN: 67978

Other (OTH) AF: 0.351 AC: 740 AN: 2110

Alfa AF: 0.162 Hom.: 268

Bravo AF: 0.339

Asia WGS AF: 0.615 AC: 2138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.7
DANN	Benign	0.43
PhyloP100		0.59

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: rs16951358;

hg19: chr15-68153732;