chr6-33058333-A-C

Variant names:

• chr6-33058333-A-C
• rs422544

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 0.299 in 148,430 control chromosomes in the GnomAD database, including 7,216 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 0.30 (7216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.405 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: 0.299 AC: 44372 AN: 148306 Hom.: 7189 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.299 AC: 44443 AN: 148430 Hom.: 7216 Cov.: 32 AF XY: 0.305 AC XY: 22133 AN XY: 72480

African (AFR) AF: 0.306 AC: 12068 AN: 39426

American (AMR) AF: 0.413 AC: 6174 AN: 14934

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1234 AN: 3436

East Asian (EAS) AF: 0.201 AC: 988 AN: 4918

South Asian (SAS) AF: 0.297 AC: 1379 AN: 4648

European-Finnish (FIN) AF: 0.341 AC: 3580 AN: 10504

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18103 AN: 67320

Other (OTH) AF: 0.326 AC: 666 AN: 2040

Alfa AF: 0.285 Hom.: 20378

Bravo AF: 0.310

Asia WGS AF: 0.287 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.7
DANN	Benign	0.40
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs422544; hg19: chr6-33026110;