11-5252457-T-G

Variant names:

• chr11-5252457-T-G
• rs2855125
• ENST00000642908.1:c.315+1835A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642908.1(ENSG00000284931):​c.315+1835A>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 151,932 control chromosomes in the GnomAD database, including 15,778 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 (15778 hom., cov: 32)
• Consequence: ENSG00000284931 ENST00000642908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

Genes affected

ENSG00000284931 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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+1835A>C		intron_variant	Intron 2 of 2			ENSP00000495346.1
ENSG00000284931	ENST00000647543.1	c.378+886A>C		intron_variant	Intron 3 of 3			ENSP00000496470.1

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65843 AN: 151814 Hom.: 15766 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.464

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: 65898 AN: 151932 Hom.: 15778 Cov.: 32 AF XY: 0.440 AC XY: 32656 AN XY: 74236

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.492

Alfa AF: 0.282 Hom.: 820

Bravo AF: 0.432

Asia WGS AF: 0.600 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2855125; hg19: chr11-5273687;