chr6-120855351-G-A

Position:

• chr6-120855351-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 0.302 in 151,970 control chromosomes in the GnomAD database, including 7,289 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 0.30 (7289 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

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 = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45902 AN: 151852 Hom.: 7281 Cov.: 33

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.302 AC: 45926 AN: 151970 Hom.: 7289 Cov.: 33 AF XY: 0.305 AC XY: 22684 AN XY: 74288

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.315

Alfa AF: 0.271 Hom.: 4226

Bravo AF: 0.317

Asia WGS AF: 0.431 AC: 1494 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	9.8
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9320773; hg19: chr6-121176497; COSMIC: COSV60275962;