rs16873952

Variant names:

• chr4-23630520-G-A
• rs16873952
• ENST00000514290.1:n.117+69481G>A

Variant summary

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

The ENST00000514290.1(ENSG00000250137):​n.117+69481G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,068 control chromosomes in the GnomAD database, including 1,475 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 0.14 (1475 hom., cov: 32)
• Consequence: ENSG00000250137 ENST00000514290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 0 publications found

Genes affected

ENSG00000250137 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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
ENSG00000250137	ENST00000514290.1	n.117+69481G>A		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20778 AN: 151950 Hom.: 1476 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.0759

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.137 AC: 20801 AN: 152068 Hom.: 1475 Cov.: 32 AF XY: 0.136 AC XY: 10117 AN XY: 74350

African (AFR) AF: 0.178 AC: 7402 AN: 41486

American (AMR) AF: 0.0892 AC: 1360 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0706 AC: 245 AN: 3470

East Asian (EAS) AF: 0.0761 AC: 392 AN: 5152

South Asian (SAS) AF: 0.135 AC: 650 AN: 4828

European-Finnish (FIN) AF: 0.152 AC: 1610 AN: 10586

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8782 AN: 67980

Other (OTH) AF: 0.116 AC: 244 AN: 2112

Alfa AF: 0.130 Hom.: 4049

Bravo AF: 0.133

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.37
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs16873952; hg19: chr4-23632143;