chr8-127516984-G-T

Variant names:

• chr8-127516984-G-T
• rs4242385

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 0.806 in 152,032 control chromosomes in the GnomAD database, including 50,147 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 0.81 (50147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 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: 0.806 AC: 122485 AN: 151914 Hom.: 50130 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.806 AC: 122543 AN: 152032 Hom.: 50147 Cov.: 32 AF XY: 0.805 AC XY: 59814 AN XY: 74290

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.839

Alfa AF: 0.849 Hom.: 15351

Bravo AF: 0.801

Asia WGS AF: 0.740 AC: 2579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4242385; hg19: chr8-128529229;