6-129763223-C-A

Variant names:

• chr6-129763223-C-A
• rs208872

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.920 AC: 25522 AN: 27740

American (AMR) AF: 0.931 AC: 9946 AN: 10684

Ashkenazi Jewish (ASJ) AF: 0.944 AC: 2684 AN: 2844

East Asian (EAS) AF: 0.998 AC: 3382 AN: 3388

South Asian (SAS) AF: 0.972 AC: 2879 AN: 2962

European-Finnish (FIN) AF: 0.921 AC: 6082 AN: 6604

Middle Eastern (MID) AF: 0.865 AC: 192 AN: 222

European-Non Finnish (NFE) AF: 0.921 AC: 50605 AN: 54924

Other (OTH) AF: 0.916 AC: 1343 AN: 1466

Alfa AF: 0.917 Hom.: 80535

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs208872; hg19: chr6-130084368;