rs11676467

Variant names:

• chr2-7693130-C-T
• rs11676467
• ENST00000414654.2:n.250+951G>A

Variant summary

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

The ENST00000414654.2(ENSG00000230515):​n.250+951G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,206 control chromosomes in the GnomAD database, including 3,643 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 0.19 (3643 hom., cov: 33)
• Consequence: ENSG00000230515 ENST00000414654.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

Genes affected

ENSG00000230515 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000414654.2. 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
	ENSG00000230515	ENST00000414654.2	TSL:2	n.250+951G>A		intron	N/A
	ENSG00000230515	ENST00000811583.1		n.146+9479G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28509 AN: 152088 Hom.: 3622 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.188 AC: 28594 AN: 152206 Hom.: 3643 Cov.: 33 AF XY: 0.186 AC XY: 13851 AN XY: 74414

African (AFR) AF: 0.355 AC: 14731 AN: 41502

American (AMR) AF: 0.104 AC: 1593 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3470

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5184

South Asian (SAS) AF: 0.142 AC: 686 AN: 4822

European-Finnish (FIN) AF: 0.169 AC: 1794 AN: 10592

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8717 AN: 68020

Other (OTH) AF: 0.171 AC: 362 AN: 2114

Alfa AF: 0.144 Hom.: 7967

Bravo AF: 0.188

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.30
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11676467; hg19: chr2-7833261;