rs1009130

Variant names:

• chr6-61054143-G-A
• rs1009130

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 0.211 in 152,080 control chromosomes in the GnomAD database, including 4,218 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 0.21 (4218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 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: 0.211 AC: 32101 AN: 151962 Hom.: 4220 Cov.: 32

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.211 AC: 32087 AN: 152080 Hom.: 4218 Cov.: 32 AF XY: 0.212 AC XY: 15727 AN XY: 74330

Gnomad4 AFR AF: 0.0588

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.230

Alfa AF: 0.276 Hom.: 5946

Bravo AF: 0.194

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1009130; hg19: chr6-58021890;