rs4937523

Variant names:

• chr11-130477295-G-T
• rs4937523

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 0.384 in 152,044 control chromosomes in the GnomAD database, including 11,807 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 0.38 (11807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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: 0.384 AC: 58333 AN: 151926 Hom.: 11787 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.361

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.384 AC: 58402 AN: 152044 Hom.: 11807 Cov.: 32 AF XY: 0.387 AC XY: 28749 AN XY: 74300

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.361

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.386

Alfa AF: 0.328 Hom.: 17298

Bravo AF: 0.389

Asia WGS AF: 0.451 AC: 1563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4937523; hg19: chr11-130347190;