rs10858373

Variant names:

• chr9-135235895-A-G
• rs10858373
• ENST00000452377.1:n.54+1649T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-135235895-A-G
• chr9-135235895-A-T

Variant summary

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

The ENST00000452377.1(ENSG00000227958):​n.54+1649T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,248 control chromosomes in the GnomAD database, including 3,463 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 0.20 (3463 hom., cov: 33)
• Consequence: ENSG00000227958 ENST00000452377.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.794

Genes affected

ENSG00000227958 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.258 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
ENSG00000227958	ENST00000452377.1	n.54+1649T>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30203 AN: 152130 Hom.: 3464 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0165

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.198 AC: 30209 AN: 152248 Hom.: 3463 Cov.: 33 AF XY: 0.195 AC XY: 14518 AN XY: 74432

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.0778

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.217

Alfa AF: 0.220 Hom.: 2374

Bravo AF: 0.188

Asia WGS AF: 0.0600 AC: 212 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	4.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10858373; hg19: chr9-138127741;