rs12502502

Variant names:

• chr4-69197032-G-A
• rs12502502
• ENST00000504301.5:n.377+1261G>A

Variant summary

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

The ENST00000504301.5(ENSG00000250696):​n.377+1261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,744 control chromosomes in the GnomAD database, including 1,482 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 0.13 (1482 hom., cov: 32)
• Consequence: ENSG00000250696 ENST00000504301.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 0 publications found

Genes affected

ENSG00000250696 (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 (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377267	NR_136191.1	n.377+1261G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250696	ENST00000504301.5	n.377+1261G>A		intron_variant	Intron 2 of 4	5
ENSG00000250696	ENST00000766439.1	n.245-3440G>A		intron_variant	Intron 1 of 3
ENSG00000250696	ENST00000766440.1	n.245-3440G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20088 AN: 151626 Hom.: 1482 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0455

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.132 AC: 20101 AN: 151744 Hom.: 1482 Cov.: 32 AF XY: 0.138 AC XY: 10258 AN XY: 74132

African (AFR) AF: 0.173 AC: 7182 AN: 41396

American (AMR) AF: 0.149 AC: 2268 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3468

East Asian (EAS) AF: 0.0452 AC: 230 AN: 5092

South Asian (SAS) AF: 0.156 AC: 749 AN: 4806

European-Finnish (FIN) AF: 0.215 AC: 2268 AN: 10568

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0969 AC: 6576 AN: 67872

Other (OTH) AF: 0.135 AC: 285 AN: 2112

Alfa AF: 0.129 Hom.: 210

Bravo AF: 0.130

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.79
PhyloP100		0.12

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12502502; hg19: chr4-70062750;