6-28843040-C-T

Variant names:

• chr6-28843040-C-T
• rs422331

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 0.377 in 151,914 control chromosomes in the GnomAD database, including 10,948 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 0.38 (10948 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57204 AN: 151796 Hom.: 10949 Cov.: 31

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.377 AC: 57225 AN: 151914 Hom.: 10948 Cov.: 31 AF XY: 0.377 AC XY: 27967 AN XY: 74226

African (AFR) AF: 0.380 AC: 15739 AN: 41430

American (AMR) AF: 0.380 AC: 5791 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1253 AN: 3466

East Asian (EAS) AF: 0.530 AC: 2729 AN: 5148

South Asian (SAS) AF: 0.427 AC: 2054 AN: 4814

European-Finnish (FIN) AF: 0.296 AC: 3113 AN: 10532

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25125 AN: 67970

Other (OTH) AF: 0.362 AC: 762 AN: 2106

Alfa AF: 0.369 Hom.: 11686

Bravo AF: 0.383

Asia WGS AF: 0.440 AC: 1529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.36
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs422331; hg19: chr6-28810817;