5-83877774-C-T

Position:

• chr5-83877774-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 0.753 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;