chr6-33807669-A-G

Variant names:

• chr6-33807669-A-G
• rs1547668

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 0.812 in 152,190 control chromosomes in the GnomAD database, including 50,361 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 0.81 (50361 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 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: 0.812 AC: 123436 AN: 152072 Hom.: 50323 Cov.: 33

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.823

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.812 AC: 123530 AN: 152190 Hom.: 50361 Cov.: 33 AF XY: 0.819 AC XY: 60923 AN XY: 74422

African (AFR) AF: 0.768 AC: 31865 AN: 41480

American (AMR) AF: 0.860 AC: 13162 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 2855 AN: 3468

East Asian (EAS) AF: 0.975 AC: 5053 AN: 5184

South Asian (SAS) AF: 0.929 AC: 4489 AN: 4832

European-Finnish (FIN) AF: 0.861 AC: 9126 AN: 10600

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.798 AC: 54288 AN: 68016

Other (OTH) AF: 0.812 AC: 1711 AN: 2108

Alfa AF: 0.810 Hom.: 105787

Bravo AF: 0.809

Asia WGS AF: 0.930 AC: 3236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs1547668; hg19: chr6-33775446;