chr8-127516190-G-C

Variant names:

• chr8-127516190-G-C
• rs4582524

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 0.908 in 152,100 control chromosomes in the GnomAD database, including 62,849 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 0.91 (62849 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 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: 0.908 AC: 138059 AN: 151982 Hom.: 62801 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.908 AC: 138163 AN: 152100 Hom.: 62849 Cov.: 32 AF XY: 0.906 AC XY: 67308 AN XY: 74316

African (AFR) AF: 0.938 AC: 38975 AN: 41546

American (AMR) AF: 0.928 AC: 14180 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3256 AN: 3472

East Asian (EAS) AF: 0.857 AC: 4444 AN: 5184

South Asian (SAS) AF: 0.868 AC: 4178 AN: 4814

European-Finnish (FIN) AF: 0.838 AC: 8802 AN: 10498

Middle Eastern (MID) AF: 0.955 AC: 279 AN: 292

European-Non Finnish (NFE) AF: 0.901 AC: 61292 AN: 67990

Other (OTH) AF: 0.915 AC: 1933 AN: 2112

Alfa AF: 0.899 Hom.: 7172

Bravo AF: 0.916

Asia WGS AF: 0.832 AC: 2875 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.33
DANN	Benign	0.25
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs4582524; hg19: chr8-128528435;