rs2855038

Variant names:

• chr11-5250924-T-C
• rs2855038
• ENST00000642908.1:c.316-2437A>G

Variant summary

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

The ENST00000642908.1(ENSG00000284931):​c.316-2437A>G 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 152,000 control chromosomes in the GnomAD database, including 15,565 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 (15565 hom., cov: 32)
• Consequence: ENSG00000284931 ENST00000642908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569

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 = 0.758 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.316-2437A>G		intron_variant	Intron 2 of 2			ENSP00000495346.1
ENSG00000284931	ENST00000647543.1	c.378+2419A>G		intron_variant	Intron 3 of 3			ENSP00000496470.1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65039 AN: 151882 Hom.: 15550 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.604

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: 0.428 AC: 65092 AN: 152000 Hom.: 15565 Cov.: 32 AF XY: 0.435 AC XY: 32285 AN XY: 74290

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.573

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.491

Alfa AF: 0.433 Hom.: 1881

Bravo AF: 0.425

Asia WGS AF: 0.597 AC: 2075 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2855038; hg19: chr11-5272154;