chr4-99322288-T-G

Variant names:

• chr4-99322288-T-G
• rs6810842

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 0.571 in 151,940 control chromosomes in the GnomAD database, including 25,692 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 0.57 (25692 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.775
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 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: 0.572 AC: 86808 AN: 151822 Hom.: 25694 Cov.: 31

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.571 AC: 86824 AN: 151940 Hom.: 25692 Cov.: 31 AF XY: 0.566 AC XY: 42004 AN XY: 74232

African (AFR) AF: 0.451 AC: 18682 AN: 41410

American (AMR) AF: 0.462 AC: 7051 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2398 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4276 AN: 5176

South Asian (SAS) AF: 0.632 AC: 3042 AN: 4814

European-Finnish (FIN) AF: 0.534 AC: 5632 AN: 10542

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43567 AN: 67960

Other (OTH) AF: 0.593 AC: 1253 AN: 2112

Alfa AF: 0.619 Hom.: 48921

Bravo AF: 0.558

Asia WGS AF: 0.591 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.69
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs6810842; hg19: chr4-100243445;