chr2-209196088-T-C

Variant names:

• chr2-209196088-T-C
• rs1583758
• ENST00000723815.1:n.183+13200A>G

Variant summary

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

The ENST00000723815.1(ENSG00000294474):​n.183+13200A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,728 control chromosomes in the GnomAD database, including 8,248 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 0.33 (8248 hom., cov: 32)
• Consequence: ENSG00000294474 ENST00000723815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 4 publications found

Genes affected

ENSG00000294474 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723815.1. 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
	ENSG00000294474	ENST00000723815.1		n.183+13200A>G		intron	N/A
	ENSG00000294474	ENST00000723816.1		n.103+12831A>G		intron	N/A
	ENSG00000294474	ENST00000723818.1		n.187-16663A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49550 AN: 151610 Hom.: 8244 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.327 AC: 49584 AN: 151728 Hom.: 8248 Cov.: 32 AF XY: 0.327 AC XY: 24261 AN XY: 74142

African (AFR) AF: 0.278 AC: 11491 AN: 41400

American (AMR) AF: 0.288 AC: 4379 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3468

East Asian (EAS) AF: 0.419 AC: 2147 AN: 5130

South Asian (SAS) AF: 0.296 AC: 1422 AN: 4812

European-Finnish (FIN) AF: 0.356 AC: 3747 AN: 10534

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24196 AN: 67882

Other (OTH) AF: 0.343 AC: 722 AN: 2102

Alfa AF: 0.230 Hom.: 729

Bravo AF: 0.322

Asia WGS AF: 0.344 AC: 1191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.71
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1583758; hg19: chr2-210060812;