rs2918206

Variant names:

• chr3-115729685-G-A
• rs2918206
• ENST00000750609.1:n.209-36435C>T

Variant summary

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

The ENST00000750609.1(ENSG00000289153):​n.209-36435C>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 151,946 control chromosomes in the GnomAD database, including 18,724 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 (18724 hom., cov: 31)
• Consequence: ENSG00000289153 ENST00000750609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816
• Publications: 2 publications found

Genes affected

ENSG00000289153 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 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
ENSG00000289153	ENST00000750609.1	n.209-36435C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73041 AN: 151828 Hom.: 18688 Cov.: 31

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.481 AC: 73123 AN: 151946 Hom.: 18724 Cov.: 31 AF XY: 0.481 AC XY: 35735 AN XY: 74270

African (AFR) AF: 0.662 AC: 27443 AN: 41436

American (AMR) AF: 0.498 AC: 7594 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1425 AN: 5168

South Asian (SAS) AF: 0.316 AC: 1521 AN: 4820

European-Finnish (FIN) AF: 0.483 AC: 5097 AN: 10554

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27294 AN: 67948

Other (OTH) AF: 0.470 AC: 990 AN: 2106

Alfa AF: 0.436 Hom.: 5107

Bravo AF: 0.490

Asia WGS AF: 0.323 AC: 1129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.18
DANN	Benign	0.40
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2918206; hg19: chr3-115448532;