6-33091175-G-A

Variant names:

• chr6-33091175-G-A
• rs10484569

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 0.062 in 152,190 control chromosomes in the GnomAD database, including 706 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 0.062 (706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.597
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0618 AC: 9401 AN: 152072 Hom.: 694 Cov.: 32

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0613

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

GnomAD4 genome AF: 0.0620 AC: 9430 AN: 152190 Hom.: 706 Cov.: 32 AF XY: 0.0620 AC XY: 4611 AN XY: 74410

African (AFR) AF: 0.0837 AC: 3473 AN: 41514

American (AMR) AF: 0.0411 AC: 629 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0351 AC: 122 AN: 3472

East Asian (EAS) AF: 0.415 AC: 2153 AN: 5182

South Asian (SAS) AF: 0.0226 AC: 109 AN: 4828

European-Finnish (FIN) AF: 0.0321 AC: 340 AN: 10582

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0357 AC: 2431 AN: 68002

Other (OTH) AF: 0.0711 AC: 150 AN: 2110

Alfa AF: 0.0447 Hom.: 925

Bravo AF: 0.0652

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
DANN	Benign	0.27
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10484569; hg19: chr6-33058952;