5-83877774-C-T

Variant names:

• chr5-83877774-C-T
• rs4552569

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 0.753 in 152,060 control chromosomes in the GnomAD database, including 43,164 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 0.75 (43164 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.782 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: 0.753 AC: 114425 AN: 151942 Hom.: 43131 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.753 AC: 114504 AN: 152060 Hom.: 43164 Cov.: 32 AF XY: 0.753 AC XY: 56007 AN XY: 74340

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.724

Alfa AF: 0.745 Hom.: 94707

Bravo AF: 0.747

Asia WGS AF: 0.783 AC: 2724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4552569; hg19: chr5-83173593;