chr4-28831166-T-C

Variant names:

• chr4-28831166-T-C
• rs6833159

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 0.294 in 152,098 control chromosomes in the GnomAD database, including 6,764 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 0.29 (6764 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 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: 0.294 AC: 44667 AN: 151980 Hom.: 6758 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.294 AC: 44696 AN: 152098 Hom.: 6764 Cov.: 32 AF XY: 0.290 AC XY: 21578 AN XY: 74342

African (AFR) AF: 0.250 AC: 10398 AN: 41514

American (AMR) AF: 0.287 AC: 4380 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 876 AN: 3466

East Asian (EAS) AF: 0.135 AC: 695 AN: 5164

South Asian (SAS) AF: 0.246 AC: 1181 AN: 4810

European-Finnish (FIN) AF: 0.329 AC: 3471 AN: 10564

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22803 AN: 67976

Other (OTH) AF: 0.286 AC: 605 AN: 2114

Alfa AF: 0.314 Hom.: 14403

Bravo AF: 0.285

Asia WGS AF: 0.216 AC: 752 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs6833159; hg19: chr4-28832788;