rs719575

chr4-27077228-C-T

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 0.331 in 151,836 control chromosomes in the GnomAD database, including 8,716 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 0.33 (8716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50169 AN: 151718 Hom.: 8711 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.331 AC: 50183 AN: 151836 Hom.: 8716 Cov.: 32 AF XY: 0.326 AC XY: 24173 AN XY: 74206

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.301

Alfa AF: 0.368 Hom.: 5278

Bravo AF: 0.321

Asia WGS AF: 0.225 AC: 781 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.9
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs719575; hg19: chr4-27078850;