11-2932493-C-T

Variant names:

• chr11-2932493-C-T
• rs3847646
• ENST00000812147.1:n.88-1463C>T

Variant summary

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

The ENST00000812147.1(ENSG00000305647):​n.88-1463C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,216 control chromosomes in the GnomAD database, including 5,794 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 0.26 (5794 hom., cov: 33)
• Consequence: ENSG00000305647 ENST00000812147.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 10 publications found

Genes affected

ENSG00000305647 (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 = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812147.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305647	ENST00000812147.1		n.88-1463C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39056 AN: 152098 Hom.: 5794 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.257 AC: 39085 AN: 152216 Hom.: 5794 Cov.: 33 AF XY: 0.257 AC XY: 19127 AN XY: 74420

African (AFR) AF: 0.205 AC: 8508 AN: 41532

American (AMR) AF: 0.347 AC: 5309 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1113 AN: 3472

East Asian (EAS) AF: 0.711 AC: 3671 AN: 5162

South Asian (SAS) AF: 0.327 AC: 1578 AN: 4822

European-Finnish (FIN) AF: 0.147 AC: 1557 AN: 10620

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16271 AN: 67988

Other (OTH) AF: 0.287 AC: 606 AN: 2114

Alfa AF: 0.242 Hom.: 568

Bravo AF: 0.272

Asia WGS AF: 0.454 AC: 1577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.44
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs3847646; hg19: chr11-2953723;