6-39290021-C-A

Position:

• chr6-39290021-C-A

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 0.27 in 152,066 control chromosomes in the GnomAD database, including 5,667 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 (5667 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 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: 0.270 AC: 40960 AN: 151948 Hom.: 5660 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.270 AC: 41004 AN: 152066 Hom.: 5667 Cov.: 32 AF XY: 0.273 AC XY: 20314 AN XY: 74312

Gnomad4 AFR AF: 0.282

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.309

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.266

Alfa AF: 0.255 Hom.: 1002

Bravo AF: 0.274

Asia WGS AF: 0.326 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9349112; hg19: chr6-39257797;