rs6824333

Variant names:

• chr4-15942287-C-T
• rs6824333

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 0.249 in 152,064 control chromosomes in the GnomAD database, including 5,688 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 0.25 (5688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.475 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: 0.249 AC: 37878 AN: 151946 Hom.: 5675 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.249 AC: 37899 AN: 152064 Hom.: 5688 Cov.: 33 AF XY: 0.257 AC XY: 19116 AN XY: 74332

African (AFR) AF: 0.100 AC: 4147 AN: 41474

American (AMR) AF: 0.407 AC: 6215 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3472

East Asian (EAS) AF: 0.325 AC: 1680 AN: 5174

South Asian (SAS) AF: 0.492 AC: 2369 AN: 4816

European-Finnish (FIN) AF: 0.252 AC: 2662 AN: 10554

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18678 AN: 67974

Other (OTH) AF: 0.260 AC: 549 AN: 2112

Alfa AF: 0.255 Hom.: 1264

Bravo AF: 0.253

Asia WGS AF: 0.380 AC: 1323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.43
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs6824333; hg19: chr4-15943910;