chr5-51015242-G-T

Variant names:

• chr5-51015242-G-T
• rs10512927
• ENST00000802600.1:n.484C>A

Variant summary

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

The ENST00000802600.1(ENSG00000304338):​n.484C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,134 control chromosomes in the GnomAD database, including 2,201 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 0.16 (2201 hom., cov: 32)
• Consequence: ENSG00000304338 ENST00000802600.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 4 publications found

Genes affected

ENSG00000304338 (HGNC:58961):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000802600.1. 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
	ENSG00000304338	ENST00000802600.1		n.484C>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000304338	ENST00000802601.1		n.614C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24281 AN: 152016 Hom.: 2199 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.160 AC: 24286 AN: 152134 Hom.: 2201 Cov.: 32 AF XY: 0.157 AC XY: 11678 AN XY: 74388

African (AFR) AF: 0.117 AC: 4867 AN: 41524

American (AMR) AF: 0.233 AC: 3563 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 730 AN: 3468

East Asian (EAS) AF: 0.0588 AC: 304 AN: 5172

South Asian (SAS) AF: 0.136 AC: 657 AN: 4814

European-Finnish (FIN) AF: 0.113 AC: 1203 AN: 10604

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12246 AN: 67978

Other (OTH) AF: 0.202 AC: 426 AN: 2104

Alfa AF: 0.106 Hom.: 208

Bravo AF: 0.167

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		0.041

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: rs10512927;

hg19: chr5-50311076;