6-147480836-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 0.605 in 151,216 control chromosomes in the GnomAD database, including 29,469 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 0.61 (29469 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

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 (NFE) allele frequency at 95% confidence interval = 0.726 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: 0.605 AC: 91469 AN: 151098 Hom.: 29453 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.657

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.605 AC: 91537 AN: 151216 Hom.: 29469 Cov.: 31 AF XY: 0.603 AC XY: 44531 AN XY: 73872

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.654

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.633

Alfa AF: 0.642 Hom.: 3497

Bravo AF: 0.589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.65
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs325109; hg19: chr6-147801972;