rs719246

Variant names:

• chr5-98722220-T-C
• rs719246

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 0.279 in 152,064 control chromosomes in the GnomAD database, including 6,343 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 0.28 (6343 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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: 0.279 AC: 42377 AN: 151946 Hom.: 6350 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.279 AC: 42368 AN: 152064 Hom.: 6343 Cov.: 32 AF XY: 0.271 AC XY: 20164 AN XY: 74342

African (AFR) AF: 0.213 AC: 8852 AN: 41496

American (AMR) AF: 0.258 AC: 3948 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3468

East Asian (EAS) AF: 0.102 AC: 529 AN: 5176

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4822

European-Finnish (FIN) AF: 0.230 AC: 2431 AN: 10578

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23132 AN: 67934

Other (OTH) AF: 0.280 AC: 590 AN: 2110

Alfa AF: 0.317 Hom.: 5357

Bravo AF: 0.281

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.52
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs719246; hg19: chr5-98057924;