chr6-39283061-G-A

Position:

• chr6-39283061-G-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 0.232 in 151,894 control chromosomes in the GnomAD database, including 4,567 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 0.23 (4567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35185 AN: 151778 Hom.: 4564 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00620

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.232 AC: 35200 AN: 151894 Hom.: 4567 Cov.: 32 AF XY: 0.226 AC XY: 16760 AN XY: 74248

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.00622

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.242

Alfa AF: 0.268 Hom.: 1541

Bravo AF: 0.231

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2758886; hg19: chr6-39250837;