15-50871860-C-T

Variant names:

• chr15-50871860-C-T
• rs4142324
• ENST00000613161.4:n.425+2712G>A

Variant summary

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

The ENST00000613161.4(ENSG00000273674):​n.425+2712G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,988 control chromosomes in the GnomAD database, including 6,773 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 0.29 (6773 hom., cov: 32)
• Consequence: ENSG00000273674 ENST00000613161.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 5 publications found

Genes affected

ENSG00000273674 (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 (EAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000613161.4. 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
	ENSG00000273674	ENST00000613161.4	TSL:2	n.425+2712G>A		intron	N/A
	ENSG00000273674	ENST00000617693.4	TSL:2	n.243+2712G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44613 AN: 151870 Hom.: 6763 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.294 AC: 44658 AN: 151988 Hom.: 6773 Cov.: 32 AF XY: 0.292 AC XY: 21688 AN XY: 74292

African (AFR) AF: 0.321 AC: 13322 AN: 41442

American (AMR) AF: 0.250 AC: 3823 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2426 AN: 5180

South Asian (SAS) AF: 0.176 AC: 849 AN: 4822

European-Finnish (FIN) AF: 0.282 AC: 2970 AN: 10546

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19530 AN: 67950

Other (OTH) AF: 0.272 AC: 575 AN: 2116

Alfa AF: 0.305 Hom.: 860

Bravo AF: 0.297

Asia WGS AF: 0.294 AC: 1021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.27
PhyloP100		-0.65

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: rs4142324;

hg19: chr15-51164057;