rs1892110

Variant names:

• chr10-90697489-G-A
• rs1892110

Your query was ambiguous. Multiple possible variants found:

• chr10-90697489-G-A
• chr10-90697489-G-C
• chr10-90697489-G-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 0.259 in 152,040 control chromosomes in the GnomAD database, including 5,568 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 0.26 (5568 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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: 0.259 AC: 39411 AN: 151922 Hom.: 5558 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.259 AC: 39453 AN: 152040 Hom.: 5568 Cov.: 33 AF XY: 0.254 AC XY: 18889 AN XY: 74306

African (AFR) AF: 0.365 AC: 15146 AN: 41442

American (AMR) AF: 0.245 AC: 3742 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 869 AN: 3470

East Asian (EAS) AF: 0.158 AC: 816 AN: 5176

South Asian (SAS) AF: 0.206 AC: 994 AN: 4814

European-Finnish (FIN) AF: 0.130 AC: 1372 AN: 10570

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15760 AN: 67974

Other (OTH) AF: 0.258 AC: 544 AN: 2106

Alfa AF: 0.240 Hom.: 17846

Bravo AF: 0.271

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.69
DANN	Benign	0.66
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1892110; hg19: chr10-92457246;