rs1547668

chr6-33807669-A-Gchr6-33807669-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 0.812 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.823

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.929

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.812

Alfa AF: 0.810 Hom.: 58456

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1547668; hg19: chr6-33775446;