chr5-79517927-C-T

Variant names:

• chr5-79517927-C-T
• rs4704560

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.851 AC: 35320 AN: 41480

American (AMR) AF: 0.601 AC: 9187 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1509 AN: 3462

East Asian (EAS) AF: 0.740 AC: 3824 AN: 5170

South Asian (SAS) AF: 0.408 AC: 1964 AN: 4812

European-Finnish (FIN) AF: 0.581 AC: 6118 AN: 10534

Middle Eastern (MID) AF: 0.448 AC: 130 AN: 290

European-Non Finnish (NFE) AF: 0.426 AC: 28902 AN: 67914

Other (OTH) AF: 0.547 AC: 1155 AN: 2112

Alfa AF: 0.513 Hom.: 34136

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

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