chr6-52186311-G-A

Position:

• chr6-52186311-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 0.0182 in 1,042,394 control chromosomes in the GnomAD database, including 453 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 0.017 (60 hom., cov: 33)
  • Exomes 𝑓: 0.018 (393 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.097 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: 0.0172 AC: 2616 AN: 152082 Hom.: 56 Cov.: 33

Gnomad AFR AF: 0.00725

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0430

Gnomad ASJ AF: 0.00779

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.00786

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0122

Gnomad OTH AF: 0.0248

GnomAD4 exome AF: 0.0184 AC: 16337 AN: 890194 Hom.: 393 AF XY: 0.0176 AC XY: 8120 AN XY: 460724

Gnomad4 AFR exome AF: 0.00780

Gnomad4 AMR exome AF: 0.0670

Gnomad4 ASJ exome AF: 0.00863

Gnomad4 EAS exome AF: 0.113

Gnomad4 SAS exome AF: 0.00758

Gnomad4 FIN exome AF: 0.0131

Gnomad4 NFE exome AF: 0.0121

Gnomad4 OTH exome AF: 0.0193

GnomAD4 genome AF: 0.0173 AC: 2627 AN: 152200 Hom.: 60 Cov.: 33 AF XY: 0.0188 AC XY: 1399 AN XY: 74428

Gnomad4 AFR AF: 0.00727

Gnomad4 AMR AF: 0.0434

Gnomad4 ASJ AF: 0.00779

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.00766

Gnomad4 FIN AF: 0.0163

Gnomad4 NFE AF: 0.0122

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0141 Hom.: 41

Bravo AF: 0.0205

Asia WGS AF: 0.0600 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.4
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8193037; hg19: chr6-52051109;