6-129743525-A-G

Variant names:

• chr6-129743525-A-G
• rs10484283

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 0.0957 in 152,214 control chromosomes in the GnomAD database, including 997 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 0.096 (997 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0956 AC: 14536 AN: 152096 Hom.: 995 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0395

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0590

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.0957 AC: 14564 AN: 152214 Hom.: 997 Cov.: 31 AF XY: 0.0931 AC XY: 6928 AN XY: 74430

African (AFR) AF: 0.193 AC: 8012 AN: 41504

American (AMR) AF: 0.0702 AC: 1073 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 420 AN: 3472

East Asian (EAS) AF: 0.0395 AC: 205 AN: 5184

South Asian (SAS) AF: 0.0505 AC: 244 AN: 4828

European-Finnish (FIN) AF: 0.0307 AC: 326 AN: 10602

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0590 AC: 4014 AN: 68016

Other (OTH) AF: 0.110 AC: 233 AN: 2110

Alfa AF: 0.0753 Hom.: 1475

Bravo AF: 0.105

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.5
DANN	Benign	0.62
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs10484283; hg19: chr6-130064670;