chr6-168704664-A-C

Position:

• chr6-168704664-A-C

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 0.919 in 152,234 control chromosomes in the GnomAD database, including 64,307 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 0.92 (64307 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.168704664A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139820 AN: 152116 Hom.: 64277 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.919 AC: 139907 AN: 152234 Hom.: 64307 Cov.: 32 AF XY: 0.918 AC XY: 68349 AN XY: 74424

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.908

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.951

Gnomad4 FIN AF: 0.920

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.931

Alfa AF: 0.916 Hom.: 33935

Bravo AF: 0.919

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs599957; hg19: chr6-169104792;