10-44386887-C-G

Variant names:

• chr10-44386887-C-G
• rs2839682
• ENST00000791650.1:n.51+2711C>G

Variant summary

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

The ENST00000791650.1(ENSG00000303087):​n.51+2711C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 152,308 control chromosomes in the GnomAD database, including 488 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 0.076 (488 hom., cov: 32)
• Consequence: ENSG00000303087 ENST00000791650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557
• Publications: 5 publications found

Genes affected

ENSG00000303087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.095 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
ENSG00000303087	ENST00000791650.1	n.51+2711C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.0756 AC: 11507 AN: 152190 Hom.: 489 Cov.: 32

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0836

Gnomad ASJ AF: 0.0685

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0969

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.0755 AC: 11505 AN: 152308 Hom.: 488 Cov.: 32 AF XY: 0.0751 AC XY: 5595 AN XY: 74470

African (AFR) AF: 0.0360 AC: 1495 AN: 41584

American (AMR) AF: 0.0834 AC: 1277 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0685 AC: 238 AN: 3472

East Asian (EAS) AF: 0.0947 AC: 490 AN: 5174

South Asian (SAS) AF: 0.0671 AC: 324 AN: 4826

European-Finnish (FIN) AF: 0.0778 AC: 825 AN: 10604

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0969 AC: 6593 AN: 68018

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0221 Hom.: 12

Bravo AF: 0.0750

Asia WGS AF: 0.0650 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.0
DANN	Benign	0.43
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2839682; hg19: chr10-44882335;