rs2855040

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0541 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642908.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000284931	ENST00000642908.1		c.316-1735G>C		intron	N/A	ENSP00000495346.1
	ENSG00000284931	ENST00000647543.1		c.379-1735G>C		intron	N/A	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

African (AFR) AF: 0.0242 AC: 955 AN: 39482

American (AMR) AF: 0.0255 AC: 387 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5186

South Asian (SAS) AF: 0.0598 AC: 288 AN: 4814

European-Finnish (FIN) AF: 0.00764 AC: 81 AN: 10608

Middle Eastern (MID) AF: 0.0276 AC: 8 AN: 290

European-Non Finnish (NFE) AF: 0.0317 AC: 2158 AN: 67990

Other (OTH) AF: 0.0211 AC: 44 AN: 2090

Alfa AF: 0.0296 Hom.: 8

Bravo AF: 0.0279

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.85
DANN	Benign	0.68
PhyloP100		-0.74
PromoterAI		-0.0035	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2855040; hg19: chr11-5271452;