chr10-58505644-A-G

Variant names:

• chr10-58505644-A-G
• rs7084402

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 0.509 in 151,806 control chromosomes in the GnomAD database, including 20,085 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 0.51 (20085 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 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: 0.508 AC: 77127 AN: 151688 Hom.: 20049 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.509 AC: 77206 AN: 151806 Hom.: 20085 Cov.: 31 AF XY: 0.510 AC XY: 37866 AN XY: 74176

African (AFR) AF: 0.604 AC: 24997 AN: 41384

American (AMR) AF: 0.366 AC: 5578 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1744 AN: 3468

East Asian (EAS) AF: 0.466 AC: 2405 AN: 5156

South Asian (SAS) AF: 0.556 AC: 2678 AN: 4818

European-Finnish (FIN) AF: 0.547 AC: 5752 AN: 10524

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32496 AN: 67914

Other (OTH) AF: 0.519 AC: 1094 AN: 2108

Alfa AF: 0.508 Hom.: 11675

Bravo AF: 0.492

Asia WGS AF: 0.557 AC: 1934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.5
DANN	Benign	0.72
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs7084402; hg19: chr10-60265404;