6-33028823-G-C

Variant names:

• chr6-33028823-G-C
• rs13215763

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 0.0724 in 152,146 control chromosomes in the GnomAD database, including 412 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 0.072 (412 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0784 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: 0.0723 AC: 10997 AN: 152028 Hom.: 412 Cov.: 31

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0801

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0724 AC: 11022 AN: 152146 Hom.: 412 Cov.: 31 AF XY: 0.0721 AC XY: 5364 AN XY: 74378

African (AFR) AF: 0.0684 AC: 2840 AN: 41494

American (AMR) AF: 0.0548 AC: 837 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3472

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5182

South Asian (SAS) AF: 0.0639 AC: 308 AN: 4822

European-Finnish (FIN) AF: 0.0823 AC: 872 AN: 10594

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0802 AC: 5450 AN: 67980

Other (OTH) AF: 0.0762 AC: 161 AN: 2114

Alfa AF: 0.0248 Hom.: 14

Bravo AF: 0.0698

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.72
DANN	Benign	0.45
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs13215763; hg19: chr6-32996600;