rs422544

Positions:

• chr6-33058333-A-C
• chr6-33058333-A-T

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 0.299 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.326

Alfa AF: 0.285 Hom.: 5751

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs422544; hg19: chr6-33026110;