chr2-206818213-T-G

Variant names:

• chr2-206818213-T-G
• rs4675639
• ENST00000658291.1:n.2909+16916T>G

Variant summary

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

The ENST00000658291.1(ENSG00000229321):​n.2909+16916T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,956 control chromosomes in the GnomAD database, including 15,370 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 0.41 (15370 hom., cov: 32)
• Consequence: ENSG00000229321 ENST00000658291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.740
• Publications: 4 publications found

Genes affected

ENSG00000229321 (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 = 0.804 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
ENSG00000229321	ENST00000658291.1	n.2909+16916T>G		intron_variant	Intron 1 of 3
ENSG00000229321	ENST00000658889.1	n.2973+16916T>G		intron_variant	Intron 1 of 4
ENSG00000229321	ENST00000661657.1	n.201+11333T>G		intron_variant	Intron 1 of 2
ENSG00000229321	ENST00000765097.1	n.62+444T>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62806 AN: 151838 Hom.: 15337 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.414 AC: 62885 AN: 151956 Hom.: 15370 Cov.: 32 AF XY: 0.422 AC XY: 31350 AN XY: 74286

African (AFR) AF: 0.624 AC: 25844 AN: 41424

American (AMR) AF: 0.443 AC: 6767 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3466

East Asian (EAS) AF: 0.825 AC: 4249 AN: 5150

South Asian (SAS) AF: 0.522 AC: 2516 AN: 4820

European-Finnish (FIN) AF: 0.348 AC: 3667 AN: 10552

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17611 AN: 67964

Other (OTH) AF: 0.410 AC: 864 AN: 2106

Alfa AF: 0.377 Hom.: 1855

Bravo AF: 0.433

Asia WGS AF: 0.653 AC: 2268 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs4675639; hg19: chr2-207682937;