rs11724777

chr4-145473163-T-A

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 0.303 in 152,202 control chromosomes in the GnomAD database, including 9,004 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 0.30 (9004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 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: 0.304 AC: 46173 AN: 152084 Hom.: 9002 Cov.: 32

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0988

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.303 AC: 46172 AN: 152202 Hom.: 9004 Cov.: 32 AF XY: 0.300 AC XY: 22336 AN XY: 74404

Gnomad4 AFR AF: 0.0776

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.0981

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.302

Alfa AF: 0.372 Hom.: 1491

Bravo AF: 0.276

Asia WGS AF: 0.179 AC: 625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	6.2
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11724777; hg19: chr4-146394315;