10-78799044-A-C

Position:

• chr10-78799044-A-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 0.353 in 152,068 control chromosomes in the GnomAD database, including 9,607 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 0.35 (9607 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.269

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.382 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: 0.353 AC: 53640 AN: 151948 Hom.: 9587 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.353 AC: 53696 AN: 152068 Hom.: 9607 Cov.: 33 AF XY: 0.350 AC XY: 26035 AN XY: 74308

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.324

Alfa AF: 0.375 Hom.: 14068

Bravo AF: 0.345

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7913285; hg19: chr10-80558801;