chr8-127486259-T-C

Position:

• chr8-127486259-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 0.864 in 152,126 control chromosomes in the GnomAD database, including 57,023 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 0.86 (57023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131412 AN: 152008 Hom.: 56992 Cov.: 31

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.914

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.864 AC: 131491 AN: 152126 Hom.: 57023 Cov.: 31 AF XY: 0.862 AC XY: 64092 AN XY: 74350

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.898

Gnomad4 OTH AF: 0.879

Alfa AF: 0.871 Hom.: 7202

Bravo AF: 0.865

Asia WGS AF: 0.803 AC: 2792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4431561; hg19: chr8-128498504;