5-51367400-C-T

Variant names:

• chr5-51367400-C-T
• rs6869844

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0263

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.197

Alfa AF: 0.143 Hom.: 3135

Bravo AF: 0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6869844; hg19: chr5-50663234;