rs422544

Variant names:

• chr6-33058333-A-C
• rs422544

Your query was ambiguous. Multiple possible variants found:

• 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 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

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;