rs211452

chr6-33363204-A-Gchr6-33363204-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 0.35 in 152,108 control chromosomes in the GnomAD database, including 9,754 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 0.35 (9754 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 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: 0.350 AC: 53231 AN: 151990 Hom.: 9745 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.350 AC: 53254 AN: 152108 Hom.: 9754 Cov.: 33 AF XY: 0.350 AC XY: 26061 AN XY: 74358

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.397

Alfa AF: 0.360 Hom.: 13299

Bravo AF: 0.350

Asia WGS AF: 0.581 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	6.5
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs211452; hg19: chr6-33330981;