6-33161969-G-A

Variant names:

• chr6-33161969-G-A
• rs9380351

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 0.191 in 152,266 control chromosomes in the GnomAD database, including 3,310 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 0.19 (3310 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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: 0.191 AC: 29081 AN: 152148 Hom.: 3296 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.191 AC: 29120 AN: 152266 Hom.: 3310 Cov.: 33 AF XY: 0.196 AC XY: 14568 AN XY: 74454

African (AFR) AF: 0.151 AC: 6273 AN: 41556

American (AMR) AF: 0.302 AC: 4622 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3472

East Asian (EAS) AF: 0.478 AC: 2468 AN: 5160

South Asian (SAS) AF: 0.166 AC: 800 AN: 4828

European-Finnish (FIN) AF: 0.225 AC: 2385 AN: 10618

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11637 AN: 68008

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.185 Hom.: 11620

Bravo AF: 0.201

Asia WGS AF: 0.266 AC: 923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.92
PhyloP100		0.80

Splicing

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

Other links and lift over

dbSNP: rs9380351; hg19: chr6-33129746;