chr2-68343640-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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687213.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289156	ENST00000687213.2		n.485+853G>C		intron	N/A
	ENSG00000289156	ENST00000798127.1		n.419+853G>C		intron	N/A
	ENSG00000289156	ENST00000798128.1		n.178+1282G>C		intron	N/A

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 v4.9

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;