2-102245610-T-A

Variant names:

• chr2-102245610-T-A
• rs1558626
• ENST00000793262.1:n.*88T>A

Variant summary

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

The ENST00000793262.1(ENSG00000303263):​n.*88T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,870 control chromosomes in the GnomAD database, including 9,558 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 0.34 (9558 hom., cov: 31)
• Consequence: ENSG00000303263 ENST00000793262.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722
• Publications: 6 publications found

Genes affected

ENSG00000303263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793262.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303263	ENST00000793262.1		n.*88T>A		downstream_gene	N/A
	ENSG00000303263	ENST00000793263.1		n.*89T>A		downstream_gene	N/A
	ENSG00000303263	ENST00000793264.1		n.*88T>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51299 AN: 151752 Hom.: 9565 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.338 AC: 51303 AN: 151870 Hom.: 9558 Cov.: 31 AF XY: 0.346 AC XY: 25643 AN XY: 74204

African (AFR) AF: 0.218 AC: 9035 AN: 41410

American (AMR) AF: 0.294 AC: 4496 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 840 AN: 3472

East Asian (EAS) AF: 0.671 AC: 3460 AN: 5154

South Asian (SAS) AF: 0.595 AC: 2856 AN: 4802

European-Finnish (FIN) AF: 0.418 AC: 4400 AN: 10538

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25081 AN: 67918

Other (OTH) AF: 0.335 AC: 705 AN: 2106

Alfa AF: 0.233 Hom.: 588

Bravo AF: 0.319

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.63
DANN	Benign	0.55
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs1558626; hg19: chr2-102862070;