rs10496276

Variant names:

• chr2-82832846-T-G
• rs10496276
• ENST00000652642.1:n.400+16T>G

Variant summary

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

The ENST00000652642.1(ENSG00000286211):​n.400+16T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,166 control chromosomes in the GnomAD database, including 3,065 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 0.19 (3065 hom., cov: 32)
• Consequence: ENSG00000286211 ENST00000652642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 5 publications found

Genes affected

ENSG00000286211 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652642.1. 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
	ENSG00000286211	ENST00000652642.1		n.400+16T>G		intron	N/A
	ENSG00000286211	ENST00000801713.1		n.290+16T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28852 AN: 152048 Hom.: 3062 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0245

Gnomad SAS AF: 0.0660

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.190 AC: 28872 AN: 152166 Hom.: 3065 Cov.: 32 AF XY: 0.187 AC XY: 13946 AN XY: 74404

African (AFR) AF: 0.243 AC: 10095 AN: 41504

American (AMR) AF: 0.133 AC: 2038 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3472

East Asian (EAS) AF: 0.0245 AC: 127 AN: 5180

South Asian (SAS) AF: 0.0661 AC: 319 AN: 4826

European-Finnish (FIN) AF: 0.206 AC: 2183 AN: 10592

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12675 AN: 67996

Other (OTH) AF: 0.161 AC: 339 AN: 2108

Alfa AF: 0.184 Hom.: 11350

Bravo AF: 0.186

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.60
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs10496276; hg19: chr2-83059970;