rs10858373

Positions:

• 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, non coding transcript 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: ENST00000452377.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.794

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000452377.1	n.54+1649T>C		intron_variant, non_coding_transcript_variant		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;