6-29648045-A-G

Variant names:

• chr6-29648045-A-G
• rs3129073

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 0.162 in 152,136 control chromosomes in the GnomAD database, including 2,411 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 0.16 (2411 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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: 0.162 AC: 24664 AN: 152018 Hom.: 2399 Cov.: 32

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.162 AC: 24691 AN: 152136 Hom.: 2411 Cov.: 32 AF XY: 0.162 AC XY: 12078 AN XY: 74362

Gnomad4 AFR AF: 0.0667

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.162

Alfa AF: 0.198 Hom.: 4795

Bravo AF: 0.157

Asia WGS AF: 0.384 AC: 1338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3129073; hg19: chr6-29615822;