rs10489488

Variant names:

• chr1-55327049-G-A
• rs10489488

Your query was ambiguous. Multiple possible variants found:

• chr1-55327049-G-A
• chr1-55327049-G-C
• chr1-55327049-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 0.0211 in 150,558 control chromosomes in the GnomAD database, including 84 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 0.021 (84 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.743

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.125 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: 0.0211 AC: 3176 AN: 150442 Hom.: 84 Cov.: 32

Gnomad AFR AF: 0.00488

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0323

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0214

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0199

Gnomad OTH AF: 0.0270

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

GnomAD4 genome AF: 0.0211 AC: 3173 AN: 150558 Hom.: 84 Cov.: 32 AF XY: 0.0212 AC XY: 1564 AN XY: 73646

Gnomad4 AFR AF: 0.00486

Gnomad4 AMR AF: 0.0323

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.0222

Gnomad4 FIN AF: 0.0214

Gnomad4 NFE AF: 0.0199

Gnomad4 OTH AF: 0.0262

Alfa AF: 0.0135 Hom.: 18

Bravo AF: 0.0236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489488; hg19: chr1-55792722;