rs2855040

Variant names:

• chr11-5250222-C-G
• rs2855040
• ENST00000642908.1:c.316-1735G>C

Variant summary

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

The ENST00000642908.1(ENSG00000284931):​c.316-1735G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0271 in 149,994 control chromosomes in the GnomAD database, including 78 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 0.027 (78 hom., cov: 31)
• Consequence: ENSG00000284931 ENST00000642908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743

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 (SAS) allele frequency at 95% confidence interval = 0.0541 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.316-1735G>C		intron_variant	Intron 2 of 2			ENSP00000495346.1
ENSG00000284931	ENST00000647543.1	c.379-1735G>C		intron_variant	Intron 3 of 3			ENSP00000496470.1

Frequencies

GnomAD3 genomes AF: 0.0271 AC: 4057 AN: 149882 Hom.: 78 Cov.: 31

Gnomad AFR AF: 0.0241

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0256

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.00346

Gnomad SAS AF: 0.0596

Gnomad FIN AF: 0.00764

Gnomad MID AF: 0.0321

Gnomad NFE AF: 0.0317

Gnomad OTH AF: 0.0218

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

GnomAD4 genome AF: 0.0271 AC: 4060 AN: 149994 Hom.: 78 Cov.: 31 AF XY: 0.0266 AC XY: 1952 AN XY: 73340

Gnomad4 AFR AF: 0.0242

Gnomad4 AMR AF: 0.0255

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.0598

Gnomad4 FIN AF: 0.00764

Gnomad4 NFE AF: 0.0317

Gnomad4 OTH AF: 0.0211

Alfa AF: 0.0296 Hom.: 8

Bravo AF: 0.0279

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.85
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2855040; hg19: chr11-5271452;