rs12991703

Variant names:

• chr2-119062670-G-T
• rs12991703
• ENST00000836652.1:n.285+1158G>T

Variant summary

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

The ENST00000836652.1(ENSG00000308819):​n.285+1158G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 151,806 control chromosomes in the GnomAD database, including 18,107 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 0.48 (18107 hom., cov: 31)
• Consequence: ENSG00000308819 ENST00000836652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 3 publications found

Genes affected

ENSG00000308819 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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
ENSG00000308819	ENST00000836652.1	n.285+1158G>T		intron_variant	Intron 2 of 2
ENSG00000308819	ENST00000836653.1	n.351+1158G>T		intron_variant	Intron 3 of 3
ENSG00000308819	ENST00000836656.1	n.344+1158G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72959 AN: 151686 Hom.: 18083 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.481 AC: 73032 AN: 151806 Hom.: 18107 Cov.: 31 AF XY: 0.480 AC XY: 35582 AN XY: 74172

African (AFR) AF: 0.511 AC: 21134 AN: 41354

American (AMR) AF: 0.456 AC: 6955 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1582 AN: 3464

East Asian (EAS) AF: 0.0587 AC: 303 AN: 5160

South Asian (SAS) AF: 0.482 AC: 2313 AN: 4802

European-Finnish (FIN) AF: 0.504 AC: 5307 AN: 10520

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33844 AN: 67938

Other (OTH) AF: 0.492 AC: 1035 AN: 2104

Alfa AF: 0.494 Hom.: 2591

Bravo AF: 0.475

Asia WGS AF: 0.279 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs12991703; hg19: chr2-119820246; COSMIC: COSV60101295;