chr10-128946084-G-A

Position:

• chr10-128946084-G-A

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 0.679 in 151,984 control chromosomes in the GnomAD database, including 35,115 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 0.68 (35115 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103068 AN: 151866 Hom.: 35084 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.679 AC: 103155 AN: 151984 Hom.: 35115 Cov.: 31 AF XY: 0.675 AC XY: 50099 AN XY: 74270

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.684

Alfa AF: 0.662 Hom.: 54332

Bravo AF: 0.687

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs765934; hg19: chr10-130744348;