6-32607881-G-C

Variant names:

• chr6-32607881-G-C
• rs3021304

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 0.514 in 150,450 control chromosomes in the GnomAD database, including 20,448 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 0.51 (20448 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77242 AN: 150332 Hom.: 20428 Cov.: 29

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.514 AC: 77312 AN: 150450 Hom.: 20448 Cov.: 29 AF XY: 0.516 AC XY: 37905 AN XY: 73476

African (AFR) AF: 0.577 AC: 23613 AN: 40900

American (AMR) AF: 0.482 AC: 7329 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1734 AN: 3446

East Asian (EAS) AF: 0.614 AC: 3126 AN: 5094

South Asian (SAS) AF: 0.446 AC: 2116 AN: 4740

European-Finnish (FIN) AF: 0.572 AC: 5965 AN: 10432

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.471 AC: 31724 AN: 67342

Other (OTH) AF: 0.525 AC: 1105 AN: 2104

Alfa AF: 0.511 Hom.: 2231

Bravo AF: 0.511

Asia WGS AF: 0.504 AC: 1756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0020
DANN	Benign	0.43
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs3021304; hg19: chr6-32575658;