chr10-58064134-C-T

Variant names:

• chr10-58064134-C-T
• rs2184033

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 0.553 in 152,014 control chromosomes in the GnomAD database, including 28,193 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 0.55 (28193 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.728 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: 0.554 AC: 84133 AN: 151896 Hom.: 28205 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.553 AC: 84122 AN: 152014 Hom.: 28193 Cov.: 32 AF XY: 0.552 AC XY: 41026 AN XY: 74318

African (AFR) AF: 0.153 AC: 6320 AN: 41420

American (AMR) AF: 0.693 AC: 10598 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2239 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2776 AN: 5162

South Asian (SAS) AF: 0.699 AC: 3365 AN: 4816

European-Finnish (FIN) AF: 0.641 AC: 6770 AN: 10558

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49884 AN: 67974

Other (OTH) AF: 0.591 AC: 1251 AN: 2116

Alfa AF: 0.675 Hom.: 109447

Bravo AF: 0.538

Asia WGS AF: 0.611 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.66
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2184033; hg19: chr10-59823894;