rs11158264

Variant names:

• chr14-59583538-G-A
• rs11158264

Your query was ambiguous. Multiple possible variants found:

• chr14-59583538-G-A
• chr14-59583538-G-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 0.513 in 152,062 control chromosomes in the GnomAD database, including 23,026 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 0.51 (23026 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344

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 (EAS) allele frequency at 95% confidence interval = 0.824 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: 0.513 AC: 77978 AN: 151944 Hom.: 23028 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.513 AC: 78005 AN: 152062 Hom.: 23026 Cov.: 32 AF XY: 0.523 AC XY: 38874 AN XY: 74344

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.532

Alfa AF: 0.586 Hom.: 12681

Bravo AF: 0.488

Asia WGS AF: 0.688 AC: 2392 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	1.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11158264; hg19: chr14-60050256;