chr6-29966386-A-C

Position:

• chr6-29966386-A-C

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 0.264 in 151,844 control chromosomes in the GnomAD database, including 5,653 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 0.26 (5653 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40080 AN: 151728 Hom.: 5652 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.264 AC: 40079 AN: 151844 Hom.: 5653 Cov.: 32 AF XY: 0.264 AC XY: 19565 AN XY: 74188

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.239

Alfa AF: 0.275 Hom.: 2741

Asia WGS AF: 0.202 AC: 697 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.0
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6935053; hg19: chr6-29934163;