rs720096

Variant names:

• chr4-178629917-G-C
• rs720096

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 0.358 in 151,476 control chromosomes in the GnomAD database, including 11,605 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 0.36 (11605 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 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: 0.359 AC: 54271 AN: 151362 Hom.: 11597 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.358 AC: 54302 AN: 151476 Hom.: 11605 Cov.: 32 AF XY: 0.356 AC XY: 26364 AN XY: 74008

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.0185

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.376

Alfa AF: 0.426 Hom.: 1885

Bravo AF: 0.332

Asia WGS AF: 0.244 AC: 838 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.014
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs720096; hg19: chr4-179551071;