chr11-118864767-G-A

Variant names:

• chr11-118864767-G-A
• rs10892301
• ENST00000816613.1:n.124+2408C>T

Variant summary

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

The ENST00000816613.1(ENSG00000306274):​n.124+2408C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,916 control chromosomes in the GnomAD database, including 12,499 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 0.40 (12499 hom., cov: 31)
• Consequence: ENSG00000306274 ENST00000816613.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.628
• Publications: 10 publications found

Genes affected

ENSG00000306274 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816613.1. 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
	ENSG00000306274	ENST00000816613.1		n.124+2408C>T		intron	N/A
	ENSG00000306274	ENST00000816614.1		n.272+2408C>T		intron	N/A
	ENSG00000306274	ENST00000816615.1		n.251+5602C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60659 AN: 151796 Hom.: 12503 Cov.: 31

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.399 AC: 60658 AN: 151916 Hom.: 12499 Cov.: 31 AF XY: 0.403 AC XY: 29893 AN XY: 74252

African (AFR) AF: 0.338 AC: 14018 AN: 41444

American (AMR) AF: 0.300 AC: 4576 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1446 AN: 3466

East Asian (EAS) AF: 0.477 AC: 2461 AN: 5160

South Asian (SAS) AF: 0.628 AC: 3028 AN: 4822

European-Finnish (FIN) AF: 0.459 AC: 4833 AN: 10534

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28917 AN: 67918

Other (OTH) AF: 0.411 AC: 867 AN: 2112

Alfa AF: 0.415 Hom.: 42130

Bravo AF: 0.380

Asia WGS AF: 0.520 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	5.3
DANN	Benign	0.76
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs10892301; hg19: chr11-118735476;