6-115663255-T-G

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 0.506 in 151,944 control chromosomes in the GnomAD database, including 19,742 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 0.51 (19742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.54 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: 0.507 AC: 76905 AN: 151828 Hom.: 19732 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.506 AC: 76951 AN: 151944 Hom.: 19742 Cov.: 32 AF XY: 0.503 AC XY: 37378 AN XY: 74276

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.503

Alfa AF: 0.394 Hom.: 1056

Bravo AF: 0.511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.9
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4946111; hg19: chr6-115984419;