rs10196529

Variant names:

• chr2-22253108-A-G
• rs10196529
• ENST00000450551.1:n.71-42114T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-22253108-A-G
• chr2-22253108-A-T

Variant summary

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

The ENST00000450551.1(ENSG00000228999):​n.71-42114T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0527 in 152,034 control chromosomes in the GnomAD database, including 591 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 0.053 (591 hom., cov: 32)
• Consequence: ENSG00000228999 ENST00000450551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

ENSG00000228999 (HGNC:52636): (long intergenic non-protein coding RNA 1830)

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 = 0.159 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
ENSG00000228999	ENST00000450551.1	n.71-42114T>C		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0526 AC: 7998 AN: 151916 Hom.: 588 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0273

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.000777

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.000659

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00752

Gnomad OTH AF: 0.0506

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

GnomAD4 genome AF: 0.0527 AC: 8015 AN: 152034 Hom.: 591 Cov.: 32 AF XY: 0.0512 AC XY: 3804 AN XY: 74334

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0272

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.000779

Gnomad4 SAS AF: 0.0286

Gnomad4 FIN AF: 0.000659

Gnomad4 NFE AF: 0.00752

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0136 Hom.: 20

Bravo AF: 0.0603

Asia WGS AF: 0.0290 AC: 101 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	0.82
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10196529; hg19: chr2-22475980;