chr6-33497642-G-A

Variant names:

• chr6-33497642-G-A
• rs1755038

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 0.907 in 152,254 control chromosomes in the GnomAD database, including 62,747 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 0.91 (62747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.907 AC: 138046 AN: 152136 Hom.: 62696 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.907 AC: 138152 AN: 152254 Hom.: 62747 Cov.: 32 AF XY: 0.911 AC XY: 67788 AN XY: 74446

African (AFR) AF: 0.881 AC: 36591 AN: 41550

American (AMR) AF: 0.903 AC: 13814 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.985 AC: 3421 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5159 AN: 5174

South Asian (SAS) AF: 0.980 AC: 4730 AN: 4828

European-Finnish (FIN) AF: 0.926 AC: 9803 AN: 10590

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.906 AC: 61649 AN: 68024

Other (OTH) AF: 0.918 AC: 1941 AN: 2114

Alfa AF: 0.911 Hom.: 7838

Bravo AF: 0.903

Asia WGS AF: 0.963 AC: 3350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.89
PhyloP100		-0.083

Splicing

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

Other links and lift over

dbSNP: rs1755038; hg19: chr6-33465419;