6-129743525-A-G

Variant names:

• chr6-129743525-A-G
• rs10484283

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0395

Gnomad4 SAS AF: 0.0505

Gnomad4 FIN AF: 0.0307

Gnomad4 NFE AF: 0.0590

Gnomad4 OTH AF: 0.110

Alfa AF: 0.0697 Hom.: 487

Bravo AF: 0.105

Asia WGS AF: 0.0660 AC: 231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484283; hg19: chr6-130064670;