rs11724777

Variant names:

• chr4-145473163-T-A
• rs11724777

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;