10-58833982-C-T

Variant names:

• chr10-58833982-C-T
• rs7085810

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 0.782 in 152,016 control chromosomes in the GnomAD database, including 49,550 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 0.78 (49550 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.915 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: 0.782 AC: 118796 AN: 151898 Hom.: 49543 Cov.: 31

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.883

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.921

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.782 AC: 118828 AN: 152016 Hom.: 49550 Cov.: 31 AF XY: 0.782 AC XY: 58094 AN XY: 74320

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.883

Gnomad4 ASJ AF: 0.968

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.921

Gnomad4 OTH AF: 0.800

Alfa AF: 0.883 Hom.: 23398

Bravo AF: 0.771

Asia WGS AF: 0.794 AC: 2764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7085810; hg19: chr10-60593742;