rs4237559

Variant names:

• chr11-93576281-A-G
• rs4237559

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 0.49 in 151,970 control chromosomes in the GnomAD database, including 18,494 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 0.49 (18494 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.585 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: 0.490 AC: 74340 AN: 151852 Hom.: 18472 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.490 AC: 74406 AN: 151970 Hom.: 18494 Cov.: 31 AF XY: 0.489 AC XY: 36336 AN XY: 74262

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.461

Alfa AF: 0.477 Hom.: 7342

Bravo AF: 0.504

Asia WGS AF: 0.472 AC: 1645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.075
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4237559; hg19: chr11-93309447;