rs10496276

chr2-82832846-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652642.1(ENSG00000286211):n.400+16T>G variant causes a intron, non coding transcript 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: ENST00000652642.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374831	XR_001739196.1	n.308-4998T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000652642.1	n.400+16T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0245

Gnomad4 SAS AF: 0.0661

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.161

Alfa AF: 0.183 Hom.: 5545

Bravo AF: 0.186

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.95
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496276; hg19: chr2-83059970;