6-33053415-A-T

Variant names:

• chr6-33053415-A-T
• rs3128955

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 0.798 in 152,064 control chromosomes in the GnomAD database, including 48,653 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 0.80 (48653 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 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: 0.798 AC: 121196 AN: 151946 Hom.: 48616 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.798 AC: 121285 AN: 152064 Hom.: 48653 Cov.: 31 AF XY: 0.800 AC XY: 59444 AN XY: 74330

African (AFR) AF: 0.838 AC: 34761 AN: 41480

American (AMR) AF: 0.673 AC: 10278 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.873 AC: 3029 AN: 3470

East Asian (EAS) AF: 0.837 AC: 4317 AN: 5156

South Asian (SAS) AF: 0.754 AC: 3629 AN: 4816

European-Finnish (FIN) AF: 0.875 AC: 9252 AN: 10576

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.786 AC: 53468 AN: 67986

Other (OTH) AF: 0.799 AC: 1685 AN: 2110

Alfa AF: 0.797 Hom.: 6051

Bravo AF: 0.782

Asia WGS AF: 0.788 AC: 2742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.42
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs3128955; hg19: chr6-33021192;