2-68343640-G-C

Variant names:

• chr2-68343640-G-C
• rs9309413
• ENST00000687213.2:n.485+853G>C

Variant summary

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

The ENST00000687213.2(ENSG00000289156):​n.485+853G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,150 control chromosomes in the GnomAD database, including 18,244 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 (18244 hom., cov: 30)
• Consequence: ENSG00000289156 ENST00000687213.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 17 publications found

Genes affected

ENSG00000289156 (HGNC:58298):

LOC102724389 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724389	XR_940224.4	n.331+853G>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289156	ENST00000687213.2	n.485+853G>C		intron_variant	Intron 4 of 4
ENSG00000289156	ENST00000798127.1	n.419+853G>C		intron_variant	Intron 4 of 4
ENSG00000289156	ENST00000798128.1	n.178+1282G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.476 AC: 71897 AN: 151038 Hom.: 18206 Cov.: 30

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.476 AC: 71999 AN: 151150 Hom.: 18244 Cov.: 30 AF XY: 0.469 AC XY: 34610 AN XY: 73754

African (AFR) AF: 0.633 AC: 26067 AN: 41148

American (AMR) AF: 0.437 AC: 6621 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3468

East Asian (EAS) AF: 0.0867 AC: 445 AN: 5130

South Asian (SAS) AF: 0.363 AC: 1732 AN: 4768

European-Finnish (FIN) AF: 0.368 AC: 3792 AN: 10300

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30257 AN: 67878

Other (OTH) AF: 0.480 AC: 1008 AN: 2098

Alfa AF: 0.412 Hom.: 6929

Bravo AF: 0.493

Asia WGS AF: 0.319 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.44
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs9309413; hg19: chr2-68570772; COSMIC: COSV53440218;