chr10-76828987-G-C

Position:

• chr10-76828987-G-C

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 0.375 in 151,876 control chromosomes in the GnomAD database, including 11,289 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 0.37 (11289 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56909 AN: 151756 Hom.: 11285 Cov.: 31

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.375 AC: 56921 AN: 151876 Hom.: 11289 Cov.: 31 AF XY: 0.372 AC XY: 27614 AN XY: 74214

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.419

Alfa AF: 0.394 Hom.: 1509

Bravo AF: 0.371

Asia WGS AF: 0.385 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2569360; hg19: chr10-78588745;