10-59578029-C-T

Variant names:

• chr10-59578029-C-T
• rs7082987

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 0.338 in 151,868 control chromosomes in the GnomAD database, including 8,783 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 0.34 (8783 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.323
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 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: 0.338 AC: 51342 AN: 151746 Hom.: 8787 Cov.: 31

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.338 AC: 51371 AN: 151868 Hom.: 8783 Cov.: 31 AF XY: 0.334 AC XY: 24775 AN XY: 74224

African (AFR) AF: 0.384 AC: 15888 AN: 41398

American (AMR) AF: 0.286 AC: 4364 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1287 AN: 3468

East Asian (EAS) AF: 0.337 AC: 1727 AN: 5132

South Asian (SAS) AF: 0.401 AC: 1929 AN: 4806

European-Finnish (FIN) AF: 0.274 AC: 2888 AN: 10544

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22330 AN: 67944

Other (OTH) AF: 0.294 AC: 621 AN: 2114

Alfa AF: 0.333 Hom.: 23375

Bravo AF: 0.338

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.61
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs7082987; hg19: chr10-61337787;