chr6-164070022-T-C

Variant names:

• chr6-164070022-T-C
• rs206694

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 0.815 in 152,230 control chromosomes in the GnomAD database, including 50,934 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 0.82 (50934 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123959 AN: 152114 Hom.: 50881 Cov.: 33

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.815 AC: 124070 AN: 152230 Hom.: 50934 Cov.: 33 AF XY: 0.819 AC XY: 60987 AN XY: 74426

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.817

Alfa AF: 0.797 Hom.: 4508

Bravo AF: 0.823

Asia WGS AF: 0.816 AC: 2837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	14
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs206694; hg19: chr6-164491054; COSMIC: COSV60300420;