8-127509818-T-C

Variant names:

• chr8-127509818-T-C
• rs10099413

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 0.813 in 152,106 control chromosomes in the GnomAD database, including 50,618 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 (50618 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.861 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: 0.813 AC: 123551 AN: 151988 Hom.: 50596 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.800

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.813 AC: 123615 AN: 152106 Hom.: 50618 Cov.: 32 AF XY: 0.811 AC XY: 60331 AN XY: 74358

African (AFR) AF: 0.709 AC: 29390 AN: 41478

American (AMR) AF: 0.839 AC: 12831 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 3208 AN: 3470

East Asian (EAS) AF: 0.755 AC: 3908 AN: 5174

South Asian (SAS) AF: 0.832 AC: 4015 AN: 4824

European-Finnish (FIN) AF: 0.800 AC: 8431 AN: 10538

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58953 AN: 68016

Other (OTH) AF: 0.845 AC: 1782 AN: 2108

Alfa AF: 0.851 Hom.: 26630

Bravo AF: 0.808

Asia WGS AF: 0.730 AC: 2539 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.47
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10099413; hg19: chr8-128522063;