6-120074294-T-G

Position:

• chr6-120074294-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 0.0731 in 151,722 control chromosomes in the GnomAD database, including 747 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 0.073 (747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 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: 0.0731 AC: 11083 AN: 151604 Hom.: 745 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0390

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0611

Gnomad SAS AF: 0.0389

Gnomad FIN AF: 0.00819

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0319

Gnomad OTH AF: 0.0644

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

GnomAD4 genome AF: 0.0731 AC: 11087 AN: 151722 Hom.: 747 Cov.: 32 AF XY: 0.0712 AC XY: 5281 AN XY: 74164

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.0390

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.0612

Gnomad4 SAS AF: 0.0389

Gnomad4 FIN AF: 0.00819

Gnomad4 NFE AF: 0.0319

Gnomad4 OTH AF: 0.0637

Alfa AF: 0.0149 Hom.: 4

Bravo AF: 0.0794

Asia WGS AF: 0.0610 AC: 212 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484967; hg19: chr6-120395440;