6-33804558-A-G

Variant names:

• chr6-33804558-A-G
• rs2281816

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 0.278 in 152,096 control chromosomes in the GnomAD database, including 6,520 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 0.28 (6520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 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: 0.278 AC: 42204 AN: 151978 Hom.: 6520 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.278 AC: 42208 AN: 152096 Hom.: 6520 Cov.: 32 AF XY: 0.282 AC XY: 20941 AN XY: 74350

African (AFR) AF: 0.190 AC: 7865 AN: 41488

American (AMR) AF: 0.270 AC: 4125 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 817 AN: 3464

East Asian (EAS) AF: 0.663 AC: 3417 AN: 5150

South Asian (SAS) AF: 0.416 AC: 2005 AN: 4820

European-Finnish (FIN) AF: 0.319 AC: 3375 AN: 10594

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19556 AN: 67966

Other (OTH) AF: 0.276 AC: 583 AN: 2114

Alfa AF: 0.280 Hom.: 6758

Bravo AF: 0.272

Asia WGS AF: 0.446 AC: 1552 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.54
DANN	Benign	0.24
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs2281816; hg19: chr6-33772335;