chr6-29969350-A-G

Position:

• chr6-29969350-A-G

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 0.267 in 151,964 control chromosomes in the GnomAD database, including 5,744 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 0.27 (5744 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.29969350A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40506 AN: 151850 Hom.: 5743 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.267 AC: 40506 AN: 151964 Hom.: 5744 Cov.: 32 AF XY: 0.266 AC XY: 19775 AN XY: 74256

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.240

Alfa AF: 0.286 Hom.: 1332

Bravo AF: 0.260

Asia WGS AF: 0.203 AC: 702 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.88
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12206499; hg19: chr6-29937127;