rs10489135

chr1-4522139-T-C

Variant summary

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

The variant allele was found at a frequency of 0.124 in 152,124 control chromosomes in the GnomAD database, including 1,414 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 0.12 (1414 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18849 AN: 152006 Hom.: 1408 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.0548

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.124 AC: 18874 AN: 152124 Hom.: 1414 Cov.: 32 AF XY: 0.126 AC XY: 9346 AN XY: 74348

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.0543

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.132

Alfa AF: 0.134 Hom.: 312

Bravo AF: 0.136

Asia WGS AF: 0.138 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.22
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489135; hg19: chr1-4582199;