chr6-33459573-T-C

Variant names:

• chr6-33459573-T-C
• rs2772372

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 0.871 in 152,160 control chromosomes in the GnomAD database, including 58,023 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 0.87 (58023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132374 AN: 152042 Hom.: 57994 Cov.: 31

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.871 AC: 132456 AN: 152160 Hom.: 58023 Cov.: 31 AF XY: 0.873 AC XY: 64962 AN XY: 74400

African (AFR) AF: 0.768 AC: 31844 AN: 41472

American (AMR) AF: 0.887 AC: 13564 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 3274 AN: 3468

East Asian (EAS) AF: 0.981 AC: 5086 AN: 5184

South Asian (SAS) AF: 0.962 AC: 4643 AN: 4824

European-Finnish (FIN) AF: 0.923 AC: 9790 AN: 10602

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61402 AN: 68012

Other (OTH) AF: 0.888 AC: 1875 AN: 2112

Alfa AF: 0.891 Hom.: 174153

Bravo AF: 0.859

Asia WGS AF: 0.943 AC: 3281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	1.5
DANN	Benign	0.71
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs2772372; hg19: chr6-33427350;