rs720096

Variant names:

• chr4-178629917-G-C
• rs720096

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 0.358 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.155 AC: 6400 AN: 41402

American (AMR) AF: 0.319 AC: 4865 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1653 AN: 3462

East Asian (EAS) AF: 0.0185 AC: 96 AN: 5176

South Asian (SAS) AF: 0.522 AC: 2513 AN: 4812

European-Finnish (FIN) AF: 0.462 AC: 4843 AN: 10486

Middle Eastern (MID) AF: 0.436 AC: 123 AN: 282

European-Non Finnish (NFE) AF: 0.481 AC: 32499 AN: 67626

Other (OTH) AF: 0.376 AC: 787 AN: 2094

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs720096; hg19: chr4-179551071;