6-33595077-A-G

Variant names:

• chr6-33595077-A-G
• rs6929819

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 0.446 in 151,824 control chromosomes in the GnomAD database, including 15,192 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 0.45 (15192 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 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: 0.446 AC: 67671 AN: 151706 Hom.: 15182 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.446 AC: 67712 AN: 151824 Hom.: 15192 Cov.: 31 AF XY: 0.447 AC XY: 33142 AN XY: 74190

African (AFR) AF: 0.412 AC: 17054 AN: 41374

American (AMR) AF: 0.467 AC: 7120 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1662 AN: 3462

East Asian (EAS) AF: 0.394 AC: 2032 AN: 5152

South Asian (SAS) AF: 0.474 AC: 2279 AN: 4804

European-Finnish (FIN) AF: 0.465 AC: 4906 AN: 10544

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31245 AN: 67930

Other (OTH) AF: 0.396 AC: 831 AN: 2100

Alfa AF: 0.457 Hom.: 2070

Bravo AF: 0.445

Asia WGS AF: 0.385 AC: 1338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6929819; hg19: chr6-33562854; COSMIC: COSV72183034;