chr9-135235895-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000227958 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452377.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227958	ENST00000452377.1	TSL:3	n.54+1649T>C		intron	N/A

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

African (AFR) AF: 0.120 AC: 4974 AN: 41550

American (AMR) AF: 0.162 AC: 2479 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3470

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5190

South Asian (SAS) AF: 0.0778 AC: 376 AN: 4830

European-Finnish (FIN) AF: 0.302 AC: 3197 AN: 10586

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17779 AN: 68022

Other (OTH) AF: 0.217 AC: 458 AN: 2112

Alfa AF: 0.230 Hom.: 3610

Bravo AF: 0.188

Asia WGS AF: 0.0600 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.74
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs10858373; hg19: chr9-138127741;