5-125822838-C-T

Variant names:

• chr5-125822838-C-T
• rs328970
• ENST00000651847.1:n.772+4990G>A

Variant summary

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

The ENST00000651847.1(ENSG00000248752):​n.772+4990G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0395 in 152,248 control chromosomes in the GnomAD database, including 405 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 0.039 (405 hom., cov: 32)
• Consequence: ENSG00000248752 ENST00000651847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 1 publications found

Genes affected

ENSG00000248752 (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 = 0.321 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651847.1. 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
	ENSG00000248752	ENST00000651847.1		n.772+4990G>A		intron	N/A
	ENSG00000248752	ENST00000825443.1		n.301+4990G>A		intron	N/A
	ENSG00000248752	ENST00000825445.1		n.179+4990G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0393 AC: 5980 AN: 152128 Hom.: 400 Cov.: 32

Gnomad AFR AF: 0.0376

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0168

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0395 AC: 6008 AN: 152248 Hom.: 405 Cov.: 32 AF XY: 0.0416 AC XY: 3098 AN XY: 74438

African (AFR) AF: 0.0376 AC: 1562 AN: 41552

American (AMR) AF: 0.0294 AC: 449 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3472

East Asian (EAS) AF: 0.334 AC: 1720 AN: 5148

South Asian (SAS) AF: 0.131 AC: 632 AN: 4820

European-Finnish (FIN) AF: 0.0168 AC: 178 AN: 10620

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0171 AC: 1163 AN: 68024

Other (OTH) AF: 0.0402 AC: 85 AN: 2116

Alfa AF: 0.0179 Hom.: 15

Bravo AF: 0.0394

Asia WGS AF: 0.225 AC: 781 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.71
PhyloP100		-0.34

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: rs328970;

hg19: chr5-125158531;