chr6-164128680-C-T

Position:

• chr6-164128680-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 0.0728 in 152,158 control chromosomes in the GnomAD database, including 533 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 (533 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 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: 0.0727 AC: 11050 AN: 152040 Hom.: 529 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.0721

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0410

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0728 AC: 11083 AN: 152158 Hom.: 533 Cov.: 33 AF XY: 0.0757 AC XY: 5635 AN XY: 74394

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0811

Gnomad4 ASJ AF: 0.0721

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0478

Gnomad4 NFE AF: 0.0410

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0494 Hom.: 473

Bravo AF: 0.0742

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.3
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: rs9347819; hg19: chr6-164549712;