rs12693520

Variant names:

• chr2-188954230-C-T
• rs12693520
• ENST00000803235.1:n.104-13843G>A

Variant summary

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

The ENST00000803235.1(ENSG00000304419):​n.104-13843G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,236 control chromosomes in the GnomAD database, including 22,195 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 0.54 (22195 hom., cov: 31)
• Consequence: ENSG00000304419 ENST00000803235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 1 publications found

Genes affected

ENSG00000304419 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 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
ENSG00000304419	ENST00000803235.1	n.104-13843G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.536 AC: 80957 AN: 151116 Hom.: 22178 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.536 AC: 81006 AN: 151236 Hom.: 22195 Cov.: 31 AF XY: 0.539 AC XY: 39792 AN XY: 73892

African (AFR) AF: 0.412 AC: 17042 AN: 41330

American (AMR) AF: 0.543 AC: 8234 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1548 AN: 3462

East Asian (EAS) AF: 0.650 AC: 3348 AN: 5152

South Asian (SAS) AF: 0.586 AC: 2821 AN: 4818

European-Finnish (FIN) AF: 0.642 AC: 6725 AN: 10480

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39542 AN: 67528

Other (OTH) AF: 0.502 AC: 1055 AN: 2102

Alfa AF: 0.562 Hom.: 3016

Bravo AF: 0.520

Asia WGS AF: 0.634 AC: 2185 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.66
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs12693520; hg19: chr2-189818956;