2-112785383-G-A

Variant names:

• chr2-112785383-G-A
• rs1800587
• ENST00000762706.1:n.404+14487G>A

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+14487G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 152,114 control chromosomes in the GnomAD database, including 7,960 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 0.32 (7960 hom., cov: 33)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 559 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762706.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299339	ENST00000762706.1		n.404+14487G>A		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+14487G>A		intron	N/A
	ENSG00000299339	ENST00000762708.1		n.265+14487G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48202 AN: 151996 Hom.: 7944 Cov.: 33

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.0787

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.317 AC: 48262 AN: 152114 Hom.: 7960 Cov.: 33 AF XY: 0.317 AC XY: 23570 AN XY: 74352

African (AFR) AF: 0.392 AC: 16263 AN: 41490

American (AMR) AF: 0.291 AC: 4452 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1191 AN: 3470

East Asian (EAS) AF: 0.0787 AC: 408 AN: 5182

South Asian (SAS) AF: 0.291 AC: 1404 AN: 4826

European-Finnish (FIN) AF: 0.316 AC: 3340 AN: 10582

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20077 AN: 67966

Other (OTH) AF: 0.306 AC: 647 AN: 2112

Alfa AF: 0.298 Hom.: 18169

Bravo AF: 0.316

Asia WGS AF: 0.212 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.38
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1800587; hg19: chr2-113542960;