5-79517927-C-T

Variant names:

• chr5-79517927-C-T
• rs4704560

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 0.584 in 151,960 control chromosomes in the GnomAD database, including 28,544 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 0.58 (28544 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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: 0.583 AC: 88552 AN: 151842 Hom.: 28488 Cov.: 31

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.584 AC: 88674 AN: 151960 Hom.: 28544 Cov.: 31 AF XY: 0.588 AC XY: 43670 AN XY: 74264

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.547

Alfa AF: 0.465 Hom.: 17523

Bravo AF: 0.605

Asia WGS AF: 0.609 AC: 2120 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4704560; hg19: chr5-78813750; COSMIC: COSV61885074;