chr10-5851305-A-C

Variant names:

• chr10-5851305-A-C
• rs7894083

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 0.5 in 151,778 control chromosomes in the GnomAD database, including 21,186 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 0.50 (21186 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 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: 0.500 AC: 75774 AN: 151660 Hom.: 21155 Cov.: 30

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.500 AC: 75855 AN: 151778 Hom.: 21186 Cov.: 30 AF XY: 0.491 AC XY: 36398 AN XY: 74176

African (AFR) AF: 0.744 AC: 30815 AN: 41402

American (AMR) AF: 0.388 AC: 5905 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1076 AN: 3462

East Asian (EAS) AF: 0.120 AC: 617 AN: 5146

South Asian (SAS) AF: 0.261 AC: 1248 AN: 4790

European-Finnish (FIN) AF: 0.440 AC: 4614 AN: 10498

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.441 AC: 29948 AN: 67942

Other (OTH) AF: 0.500 AC: 1051 AN: 2102

Alfa AF: 0.446 Hom.: 8351

Bravo AF: 0.508

Asia WGS AF: 0.313 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.24
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7894083; hg19: chr10-5893268;