rs6733447

chr2-20975264-G-A

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 0.537 in 151,988 control chromosomes in the GnomAD database, including 22,510 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 0.54 (22510 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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: 0.538 AC: 81648 AN: 151870 Hom.: 22513 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.537 AC: 81663 AN: 151988 Hom.: 22510 Cov.: 32 AF XY: 0.539 AC XY: 40016 AN XY: 74278

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.719

Gnomad4 FIN AF: 0.520

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.558

Alfa AF: 0.539 Hom.: 3736

Bravo AF: 0.528

Asia WGS AF: 0.741 AC: 2577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.011
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6733447; hg19: chr2-21198136;