11-5251917-C-G

Variant names:

• chr11-5251917-C-G
• rs2855126
• ENST00000642908.1:c.315+2375G>C

Variant summary

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

The ENST00000642908.1(ENSG00000284931):​c.315+2375G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,848 control chromosomes in the GnomAD database, including 15,742 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 0.43 (15742 hom., cov: 32)
• Consequence: ENSG00000284931 ENST00000642908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• 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 (EAS) allele frequency at 95% confidence interval = 0.758 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+2375G>C		intron_variant	Intron 2 of 2			ENSP00000495346.1
ENSG00000284931	ENST00000647543.1	c.378+1426G>C		intron_variant	Intron 3 of 3			ENSP00000496470.1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65787 AN: 151730 Hom.: 15728 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.434 AC: 65845 AN: 151848 Hom.: 15742 Cov.: 32 AF XY: 0.440 AC XY: 32642 AN XY: 74204

African (AFR) AF: 0.248 AC: 10248 AN: 41384

American (AMR) AF: 0.576 AC: 8794 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2155 AN: 3464

East Asian (EAS) AF: 0.778 AC: 4011 AN: 5154

South Asian (SAS) AF: 0.548 AC: 2632 AN: 4802

European-Finnish (FIN) AF: 0.461 AC: 4861 AN: 10542

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31461 AN: 67936

Other (OTH) AF: 0.492 AC: 1036 AN: 2106

Alfa AF: 0.303 Hom.: 829

Bravo AF: 0.431

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.62
DANN	Benign	0.68
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2855126; hg19: chr11-5273147;