11-5251452-C-T

Variant names:

• chr11-5251452-C-T
• rs2855036
• ENST00000642908.1:c.315+2840G>A

Variant summary

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

The ENST00000642908.1(ENSG00000284931):​c.315+2840G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,558 control chromosomes in the GnomAD database, including 6,802 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 0.29 (6802 hom., cov: 31)
• Consequence: ENSG00000284931 ENST00000642908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• Publications: 5 publications found

Genes affected

ENSG00000284931 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000284931	ENST00000642908.1	c.315+2840G>A		intron_variant	Intron 2 of 2			ENSP00000495346.1
ENSG00000284931	ENST00000647543.1	c.378+1891G>A		intron_variant	Intron 3 of 3			ENSP00000496470.1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43989 AN: 151440 Hom.: 6797 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.290 AC: 44021 AN: 151558 Hom.: 6802 Cov.: 31 AF XY: 0.284 AC XY: 20987 AN XY: 74014

African (AFR) AF: 0.312 AC: 12875 AN: 41282

American (AMR) AF: 0.228 AC: 3475 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3458

East Asian (EAS) AF: 0.117 AC: 607 AN: 5168

South Asian (SAS) AF: 0.279 AC: 1337 AN: 4788

European-Finnish (FIN) AF: 0.217 AC: 2263 AN: 10436

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21875 AN: 67876

Other (OTH) AF: 0.286 AC: 605 AN: 2114

Alfa AF: 0.257 Hom.: 1301

Bravo AF: 0.290

Asia WGS AF: 0.242 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.93
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2855036; hg19: chr11-5272682;