rs140709

Positions:

• chr6-12213177-CATT-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (8730 hom., cov: 0)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.839

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.12213178_12213180delATT		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47123 AN: 151256 Hom.: 8730 Cov.: 0

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.311 AC: 47131 AN: 151366 Hom.: 8730 Cov.: 0 AF XY: 0.315 AC XY: 23270 AN XY: 73902

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.285

Alfa AF: 0.332 Hom.: 911

Asia WGS AF: 0.323 AC: 1123 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs140709; hg19: chr6-12213410;