2-205627674-C-T

Variant names:

• chr2-205627674-C-T
• rs888090
• ENST00000792092.1:n.578+1347G>A

Variant summary

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

The ENST00000792092.1(ENSG00000303132):​n.578+1347G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,012 control chromosomes in the GnomAD database, including 17,577 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 0.47 (17577 hom., cov: 32)
• Consequence: ENSG00000303132 ENST00000792092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 3 publications found

Genes affected

ENSG00000303132 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000792092.1. 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
	ENSG00000303132	ENST00000792092.1		n.578+1347G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71871 AN: 151894 Hom.: 17537 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.473 AC: 71957 AN: 152012 Hom.: 17577 Cov.: 32 AF XY: 0.480 AC XY: 35694 AN XY: 74330

African (AFR) AF: 0.393 AC: 16294 AN: 41454

American (AMR) AF: 0.593 AC: 9076 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1420 AN: 3470

East Asian (EAS) AF: 0.646 AC: 3344 AN: 5180

South Asian (SAS) AF: 0.484 AC: 2332 AN: 4820

European-Finnish (FIN) AF: 0.619 AC: 6535 AN: 10564

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31307 AN: 67924

Other (OTH) AF: 0.462 AC: 971 AN: 2104

Alfa AF: 0.466 Hom.: 14811

Bravo AF: 0.474

Asia WGS AF: 0.565 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.34
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs888090; hg19: chr2-206492398;