rs10890324

Variant names:

• chr1-45325482-G-A
• rs10890324

Your query was ambiguous. Multiple possible variants found:

• chr1-45325482-G-A
• chr1-45325482-G-C
• chr1-45325482-G-T

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 0.619 in 151,978 control chromosomes in the GnomAD database, including 32,076 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 0.62 (32076 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 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: 0.619 AC: 94014 AN: 151860 Hom.: 32074 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.736

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.619 AC: 94022 AN: 151978 Hom.: 32076 Cov.: 32 AF XY: 0.626 AC XY: 46504 AN XY: 74300

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.671

Alfa AF: 0.711 Hom.: 52727

Bravo AF: 0.604

Asia WGS AF: 0.762 AC: 2646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10890324; hg19: chr1-45791154;