chr6-164070022-T-C

Position:

• chr6-164070022-T-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 0.815 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;