chr5-51967667-C-T

Variant names:

• chr5-51967667-C-T
• rs10051973

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 0.888 in 152,142 control chromosomes in the GnomAD database, including 60,872 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 0.89 (60872 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135093 AN: 152024 Hom.: 60851 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.888 AC: 135162 AN: 152142 Hom.: 60872 Cov.: 32 AF XY: 0.889 AC XY: 66100 AN XY: 74378

African (AFR) AF: 0.719 AC: 29815 AN: 41468

American (AMR) AF: 0.937 AC: 14292 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3290 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5167 AN: 5168

South Asian (SAS) AF: 0.951 AC: 4588 AN: 4822

European-Finnish (FIN) AF: 0.930 AC: 9873 AN: 10614

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.959 AC: 65211 AN: 68022

Other (OTH) AF: 0.899 AC: 1900 AN: 2114

Alfa AF: 0.938 Hom.: 85410

Bravo AF: 0.882

Asia WGS AF: 0.961 AC: 3342 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.81
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10051973; hg19: chr5-51263501; COSMIC: COSV60127395;