rs10489135

Variant names:

• chr1-4522139-T-C
• rs10489135

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.123 AC: 5111 AN: 41488

American (AMR) AF: 0.230 AC: 3523 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3472

East Asian (EAS) AF: 0.228 AC: 1173 AN: 5154

South Asian (SAS) AF: 0.0543 AC: 262 AN: 4828

European-Finnish (FIN) AF: 0.122 AC: 1286 AN: 10576

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7012 AN: 68000

Other (OTH) AF: 0.132 AC: 279 AN: 2112

Alfa AF: 0.134 Hom.: 322

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10489135; hg19: chr1-4582199;