8-127486259-T-C

Variant names:

• chr8-127486259-T-C
• rs4431561

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;