10-78799044-A-C

Variant names:

• chr10-78799044-A-C
• rs7913285

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 0.353 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.323 AC: 13405 AN: 41470

American (AMR) AF: 0.324 AC: 4959 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1139 AN: 3468

East Asian (EAS) AF: 0.289 AC: 1494 AN: 5162

South Asian (SAS) AF: 0.357 AC: 1720 AN: 4824

European-Finnish (FIN) AF: 0.361 AC: 3815 AN: 10572

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26223 AN: 67968

Other (OTH) AF: 0.324 AC: 682 AN: 2108

Alfa AF: 0.372 Hom.: 17339

Bravo AF: 0.345

Asia WGS AF: 0.307 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7913285; hg19: chr10-80558801;