5-159308925-G-A

Variant names:

• chr5-159308925-G-A
• rs4921468
• ENST00000765301.1:n.221+1532C>T

Variant summary

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

The ENST00000765301.1(ENSG00000299638):​n.221+1532C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,098 control chromosomes in the GnomAD database, including 5,319 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 0.26 (5319 hom., cov: 32)
• Consequence: ENSG00000299638 ENST00000765301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 11 publications found

Genes affected

ENSG00000299638 (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 (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765301.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299638	ENST00000765301.1		n.221+1532C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39296 AN: 151980 Hom.: 5312 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.259 AC: 39327 AN: 152098 Hom.: 5319 Cov.: 32 AF XY: 0.257 AC XY: 19130 AN XY: 74344

African (AFR) AF: 0.183 AC: 7592 AN: 41486

American (AMR) AF: 0.269 AC: 4112 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3472

East Asian (EAS) AF: 0.231 AC: 1194 AN: 5174

South Asian (SAS) AF: 0.183 AC: 883 AN: 4822

European-Finnish (FIN) AF: 0.318 AC: 3367 AN: 10574

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19896 AN: 67970

Other (OTH) AF: 0.291 AC: 614 AN: 2108

Alfa AF: 0.285 Hom.: 27202

Bravo AF: 0.257

Asia WGS AF: 0.222 AC: 772 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	2.7
DANN	Benign	0.31
PhyloP100		-0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4921468; hg19: chr5-158735933;