rs601006

Variant names:

• chr6-32605396-G-A
• rs601006

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 0.321 in 148,182 control chromosomes in the GnomAD database, including 8,132 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 0.32 (8132 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.273

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 (AMR) allele frequency at 95% confidence interval = 0.379 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: 0.321 AC: 47556 AN: 148068 Hom.: 8133 Cov.: 24

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.327

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.321 AC: 47580 AN: 148182 Hom.: 8132 Cov.: 24 AF XY: 0.317 AC XY: 22865 AN XY: 72218

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.363

Gnomad4 OTH AF: 0.331

Alfa AF: 0.321 Hom.: 890

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	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs601006; hg19: chr6-32573173;