5-51367400-C-T

Variant names:

• chr5-51367400-C-T
• rs6869844

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 0.201 in 152,038 control chromosomes in the GnomAD database, including 3,977 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 0.20 (3977 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.201 AC: 30499 AN: 151920 Hom.: 3964 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0265

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.201 AC: 30523 AN: 152038 Hom.: 3977 Cov.: 32 AF XY: 0.198 AC XY: 14704 AN XY: 74310

African (AFR) AF: 0.365 AC: 15129 AN: 41428

American (AMR) AF: 0.123 AC: 1882 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.0263 AC: 136 AN: 5164

South Asian (SAS) AF: 0.180 AC: 866 AN: 4814

European-Finnish (FIN) AF: 0.160 AC: 1698 AN: 10586

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9730 AN: 67980

Other (OTH) AF: 0.197 AC: 416 AN: 2112

Alfa AF: 0.156 Hom.: 6324

Bravo AF: 0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs6869844; hg19: chr5-50663234;