chr5-56415464-C-T

Variant names:

• chr5-56415464-C-T
• rs158214

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 0.553 in 151,996 control chromosomes in the GnomAD database, including 24,725 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 0.55 (24725 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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 (NFE) allele frequency at 95% confidence interval = 0.646 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: 0.553 AC: 84049 AN: 151878 Hom.: 24721 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.553 AC: 84067 AN: 151996 Hom.: 24725 Cov.: 31 AF XY: 0.556 AC XY: 41331 AN XY: 74274

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.750

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.618

Alfa AF: 0.640 Hom.: 65044

Bravo AF: 0.534

Asia WGS AF: 0.563 AC: 1957 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	1.1
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs158214; hg19: chr5-55711291;