rs10489074

Variant names:

• chr4-10270981-C-A
• rs10489074

Your query was ambiguous. Multiple possible variants found:

• chr4-10270981-C-A
• chr4-10270981-C-T

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 0.199 in 152,042 control chromosomes in the GnomAD database, including 3,570 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 (3570 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.259 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: 0.200 AC: 30317 AN: 151926 Hom.: 3570 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.199 AC: 30311 AN: 152042 Hom.: 3570 Cov.: 33 AF XY: 0.197 AC XY: 14648 AN XY: 74300

African (AFR) AF: 0.116 AC: 4803 AN: 41512

American (AMR) AF: 0.143 AC: 2186 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 574 AN: 3470

East Asian (EAS) AF: 0.164 AC: 845 AN: 5164

South Asian (SAS) AF: 0.145 AC: 692 AN: 4778

European-Finnish (FIN) AF: 0.251 AC: 2646 AN: 10546

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17798 AN: 67976

Other (OTH) AF: 0.197 AC: 415 AN: 2110

Alfa AF: 0.232 Hom.: 16845

Bravo AF: 0.187

Asia WGS AF: 0.159 AC: 555 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.39
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10489074; hg19: chr4-10272605;