chr8-127516788-A-T

Variant names:

• chr8-127516788-A-T
• rs4498506

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.778 in 152,078 control chromosomes in the GnomAD database, including 47,467 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 0.78 (47467 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.874 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: 0.778 AC: 118237 AN: 151960 Hom.: 47461 Cov.: 33

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.778 AC: 118281 AN: 152078 Hom.: 47467 Cov.: 33 AF XY: 0.777 AC XY: 57783 AN XY: 74320

African (AFR) AF: 0.563 AC: 23324 AN: 41452

American (AMR) AF: 0.826 AC: 12633 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3200 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3958 AN: 5176

South Asian (SAS) AF: 0.828 AC: 3992 AN: 4824

European-Finnish (FIN) AF: 0.806 AC: 8491 AN: 10536

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59867 AN: 68012

Other (OTH) AF: 0.817 AC: 1727 AN: 2114

Alfa AF: 0.818 Hom.: 6437

Bravo AF: 0.767

Asia WGS AF: 0.734 AC: 2555 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.0
DANN	Benign	0.67
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs4498506; hg19: chr8-128529033;