5-56757652-C-T

Variant names:

• chr5-56757652-C-T
• rs74345699

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 0.148 in 152,202 control chromosomes in the GnomAD database, including 2,133 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 0.15 (2133 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.444

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 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: 0.148 AC: 22539 AN: 152084 Hom.: 2122 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.148 AC: 22570 AN: 152202 Hom.: 2133 Cov.: 32 AF XY: 0.154 AC XY: 11446 AN XY: 74404

Gnomad4 AFR AF: 0.0637

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.159

Alfa AF: 0.0764 Hom.: 98

Bravo AF: 0.149

Asia WGS AF: 0.324 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs74345699; hg19: chr5-56053479;