rs2255519

Variant names:

• chr11-5252311-G-A
• rs2255519
• ENST00000642908.1:c.315+1981C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-5252311-G-A
• chr11-5252311-G-C

Variant summary

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

The ENST00000642908.1(ENSG00000284931):​c.315+1981C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,980 control chromosomes in the GnomAD database, including 15,540 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 (15540 hom., cov: 32)
• Consequence: ENSG00000284931 ENST00000642908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417

Genes affected

ENSG00000284931 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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+1981C>T		intron_variant	Intron 2 of 2			ENSP00000495346.1
ENSG00000284931	ENST00000647543.1	c.378+1032C>T		intron_variant	Intron 3 of 3			ENSP00000496470.1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65011 AN: 151862 Hom.: 15527 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.428 AC: 65061 AN: 151980 Hom.: 15540 Cov.: 32 AF XY: 0.435 AC XY: 32277 AN XY: 74266

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.490

Alfa AF: 0.455 Hom.: 6357

Bravo AF: 0.425

Asia WGS AF: 0.597 AC: 2076 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	1.5
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2255519; hg19: chr11-5273541;