chr8-109122051-A-C

Variant names:

• chr8-109122051-A-C
• rs10505126

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 0.572 in 151,298 control chromosomes in the GnomAD database, including 26,398 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 0.57 (26398 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.781 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: 0.571 AC: 86393 AN: 151180 Hom.: 26339 Cov.: 32

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.572 AC: 86516 AN: 151298 Hom.: 26398 Cov.: 32 AF XY: 0.575 AC XY: 42492 AN XY: 73878

Gnomad4 AFR AF: 0.788

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.566

Alfa AF: 0.517 Hom.: 2695

Bravo AF: 0.592

Asia WGS AF: 0.617 AC: 2140 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.9
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505126; hg19: chr8-110134280;