chr6-32605396-G-A

Variant names:

• chr6-32605396-G-A
• rs601006

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 0.321 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.249 AC: 10049 AN: 40330

American (AMR) AF: 0.387 AC: 5722 AN: 14776

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1386 AN: 3404

East Asian (EAS) AF: 0.195 AC: 987 AN: 5058

South Asian (SAS) AF: 0.302 AC: 1386 AN: 4594

European-Finnish (FIN) AF: 0.270 AC: 2739 AN: 10142

Middle Eastern (MID) AF: 0.303 AC: 88 AN: 290

European-Non Finnish (NFE) AF: 0.363 AC: 24167 AN: 66656

Other (OTH) AF: 0.331 AC: 675 AN: 2042

Alfa AF: 0.321 Hom.: 890

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs601006; hg19: chr6-32573173;