rs16902429

Variant names:

• chr5-86855803-T-G
• rs16902429
• ENST00000724121.1:n.150-34190A>C

Variant summary

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

The ENST00000724121.1(ENSG00000294529):​n.150-34190A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,076 control chromosomes in the GnomAD database, including 5,089 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 0.25 (5089 hom., cov: 32)
• Consequence: ENSG00000294529 ENST00000724121.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 2 publications found

Genes affected

ENSG00000294529 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294529	ENST00000724121.1	n.150-34190A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38074 AN: 151958 Hom.: 5090 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.250 AC: 38084 AN: 152076 Hom.: 5089 Cov.: 32 AF XY: 0.248 AC XY: 18431 AN XY: 74330

African (AFR) AF: 0.199 AC: 8266 AN: 41492

American (AMR) AF: 0.238 AC: 3627 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1170 AN: 3466

East Asian (EAS) AF: 0.0615 AC: 319 AN: 5184

South Asian (SAS) AF: 0.187 AC: 901 AN: 4820

European-Finnish (FIN) AF: 0.273 AC: 2893 AN: 10580

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20026 AN: 67960

Other (OTH) AF: 0.251 AC: 530 AN: 2110

Alfa AF: 0.277 Hom.: 23470

Bravo AF: 0.243

Asia WGS AF: 0.167 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.51
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs16902429; hg19: chr5-86151620;