6-99192734-G-A

Variant names:

• chr6-99192734-G-A
• rs7745052

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 0.219 in 151,852 control chromosomes in the GnomAD database, including 4,026 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 0.22 (4026 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33248 AN: 151732 Hom.: 4026 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.219 AC: 33270 AN: 151852 Hom.: 4026 Cov.: 31 AF XY: 0.222 AC XY: 16489 AN XY: 74214

African (AFR) AF: 0.167 AC: 6901 AN: 41404

American (AMR) AF: 0.245 AC: 3738 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3468

East Asian (EAS) AF: 0.458 AC: 2348 AN: 5130

South Asian (SAS) AF: 0.405 AC: 1944 AN: 4804

European-Finnish (FIN) AF: 0.188 AC: 1982 AN: 10570

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14791 AN: 67916

Other (OTH) AF: 0.236 AC: 498 AN: 2108

Alfa AF: 0.224 Hom.: 17245

Bravo AF: 0.219

Asia WGS AF: 0.439 AC: 1525 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.42
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs7745052; hg19: chr6-99640610;