chr5-51367400-C-T

Position:

• chr5-51367400-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;