6-130506337-C-T

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 0.144 in 151,980 control chromosomes in the GnomAD database, including 1,826 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 0.14 (1826 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 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: 0.144 AC: 21875 AN: 151862 Hom.: 1811 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.144 AC: 21926 AN: 151980 Hom.: 1826 Cov.: 31 AF XY: 0.145 AC XY: 10799 AN XY: 74270

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0821

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.155

Alfa AF: 0.107 Hom.: 945

Bravo AF: 0.156

Asia WGS AF: 0.260 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	8.3
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9402234; hg19: chr6-130827482;