rs10489070

Variant names:

• chr4-10274728-C-G
• rs10489070

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 0.173 in 152,052 control chromosomes in the GnomAD database, including 2,375 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 0.17 (2375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.234 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: 0.173 AC: 26226 AN: 151934 Hom.: 2368 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.173 AC: 26242 AN: 152052 Hom.: 2375 Cov.: 32 AF XY: 0.173 AC XY: 12824 AN XY: 74316

African (AFR) AF: 0.121 AC: 5030 AN: 41498

American (AMR) AF: 0.240 AC: 3666 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 925 AN: 3470

East Asian (EAS) AF: 0.134 AC: 689 AN: 5160

South Asian (SAS) AF: 0.135 AC: 650 AN: 4820

European-Finnish (FIN) AF: 0.168 AC: 1778 AN: 10570

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12934 AN: 67962

Other (OTH) AF: 0.180 AC: 378 AN: 2102

Alfa AF: 0.179 Hom.: 339

Bravo AF: 0.176

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.30
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs10489070; hg19: chr4-10276352;