rs2855039

Variant names:

• chr11-5250441-C-T
• rs2855039
• ENST00000642908.1:c.316-1954G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642908.1(ENSG00000284931):​c.316-1954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,048 control chromosomes in the GnomAD database, including 5,152 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 0.25 (5152 hom., cov: 32)
• Consequence: ENSG00000284931 ENST00000642908.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13
• Publications: 22 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.317 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.316-1954G>A		intron_variant	Intron 2 of 2			ENSP00000495346.1
ENSG00000284931	ENST00000647543.1	c.379-1954G>A		intron_variant	Intron 3 of 3			ENSP00000496470.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37348 AN: 151930 Hom.: 5155 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.246 AC: 37352 AN: 152048 Hom.: 5152 Cov.: 32 AF XY: 0.241 AC XY: 17889 AN XY: 74324

African (AFR) AF: 0.160 AC: 6650 AN: 41482

American (AMR) AF: 0.209 AC: 3198 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 688 AN: 3470

East Asian (EAS) AF: 0.117 AC: 608 AN: 5178

South Asian (SAS) AF: 0.278 AC: 1337 AN: 4812

European-Finnish (FIN) AF: 0.216 AC: 2283 AN: 10576

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.320 AC: 21775 AN: 67946

Other (OTH) AF: 0.253 AC: 534 AN: 2114

Alfa AF: 0.291 Hom.: 27284

Bravo AF: 0.237

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.065
DANN	Benign	0.41
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs2855039; hg19: chr11-5271671;