rs10153799

Variant names:

• chr2-57552907-T-G
• rs10153799
• ENST00000811252.1:n.56-1154A>C

Variant summary

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

The ENST00000811252.1(ENSG00000285755):​n.56-1154A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0773 in 151,928 control chromosomes in the GnomAD database, including 1,049 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 0.077 (1049 hom., cov: 32)
• Consequence: ENSG00000285755 ENST00000811252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152
• Publications: 2 publications found

Genes affected

ENSG00000285755 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811252.1. 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
	ENSG00000285755	ENST00000811252.1		n.56-1154A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11719 AN: 151810 Hom.: 1048 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0506

Gnomad ASJ AF: 0.0586

Gnomad EAS AF: 0.0794

Gnomad SAS AF: 0.0622

Gnomad FIN AF: 0.0112

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0810

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

GnomAD4 genome AF: 0.0773 AC: 11737 AN: 151928 Hom.: 1049 Cov.: 32 AF XY: 0.0763 AC XY: 5669 AN XY: 74268

African (AFR) AF: 0.213 AC: 8813 AN: 41452

American (AMR) AF: 0.0504 AC: 768 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0586 AC: 203 AN: 3466

East Asian (EAS) AF: 0.0788 AC: 404 AN: 5128

South Asian (SAS) AF: 0.0622 AC: 300 AN: 4820

European-Finnish (FIN) AF: 0.0112 AC: 119 AN: 10616

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0137 AC: 928 AN: 67906

Other (OTH) AF: 0.0802 AC: 169 AN: 2108

Alfa AF: 0.0582 Hom.: 114

Bravo AF: 0.0842

Asia WGS AF: 0.0680 AC: 236 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.1
DANN	Benign	0.39
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10153799; hg19: chr2-57780042;