rs208872

Positions:

• chr6-129763223-C-A
• chr6-129763223-C-G
• chr6-129763223-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.93 (47936 hom., cov: 13)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.129763223C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.926 AC: 103151 AN: 111438 Hom.: 47887 Cov.: 13

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.944

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.972

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.926 AC: 103258 AN: 111554 Hom.: 47936 Cov.: 13 AF XY: 0.925 AC XY: 48973 AN XY: 52916

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.944

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.972

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.916

Alfa AF: 0.917 Hom.: 69161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.52
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs208872; hg19: chr6-130084368;