chr6-164185287-A-G

Position:

• chr6-164185287-A-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 0.0796 in 152,266 control chromosomes in the GnomAD database, including 589 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 0.080 (589 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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: 0.0796 AC: 12117 AN: 152148 Hom.: 590 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0796 AC: 12117 AN: 152266 Hom.: 589 Cov.: 33 AF XY: 0.0768 AC XY: 5721 AN XY: 74448

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0487

Gnomad4 ASJ AF: 0.0234

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0735

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.0754

Gnomad4 OTH AF: 0.0657

Alfa AF: 0.0732 Hom.: 244

Bravo AF: 0.0804

Asia WGS AF: 0.0470 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484507; hg19: chr6-164606319;