chr4-87292656-A-G

Variant names:

• chr4-87292656-A-G
• rs6834314

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 0.243 in 152,042 control chromosomes in the GnomAD database, including 4,599 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 0.24 (4599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 105 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 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: 0.243 AC: 36933 AN: 151924 Hom.: 4602 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.243 AC: 36938 AN: 152042 Hom.: 4599 Cov.: 32 AF XY: 0.236 AC XY: 17571 AN XY: 74320

African (AFR) AF: 0.219 AC: 9076 AN: 41442

American (AMR) AF: 0.186 AC: 2839 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1753 AN: 5172

South Asian (SAS) AF: 0.175 AC: 841 AN: 4812

European-Finnish (FIN) AF: 0.218 AC: 2311 AN: 10582

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18586 AN: 67968

Other (OTH) AF: 0.223 AC: 470 AN: 2112

Alfa AF: 0.247 Hom.: 628

Bravo AF: 0.241

Asia WGS AF: 0.246 AC: 854 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.5
DANN	Benign	0.92
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6834314; hg19: chr4-88213808;