rs327837

Variant names:

• chr5-125829498-G-A
• rs327837
• ENST00000651847.1:n.594-1492C>T

Variant summary

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

The ENST00000651847.1(ENSG00000248752):​n.594-1492C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,014 control chromosomes in the GnomAD database, including 9,407 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 0.35 (9407 hom., cov: 32)
• Consequence: ENSG00000248752 ENST00000651847.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 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.594-1492C>T		intron	N/A
	ENSG00000248752	ENST00000825443.1		n.123-1492C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52479 AN: 151894 Hom.: 9409 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.345 AC: 52493 AN: 152014 Hom.: 9407 Cov.: 32 AF XY: 0.343 AC XY: 25492 AN XY: 74282

African (AFR) AF: 0.264 AC: 10971 AN: 41492

American (AMR) AF: 0.349 AC: 5334 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1517 AN: 3472

East Asian (EAS) AF: 0.333 AC: 1712 AN: 5146

South Asian (SAS) AF: 0.437 AC: 2105 AN: 4820

European-Finnish (FIN) AF: 0.305 AC: 3224 AN: 10560

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26373 AN: 67946

Other (OTH) AF: 0.362 AC: 765 AN: 2112

Alfa AF: 0.375 Hom.: 2225

Bravo AF: 0.341

Asia WGS AF: 0.325 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		-0.23

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: rs327837;

hg19: chr5-125165191;

COSMIC: COSV60195100;