chr14-59583538-G-A

Variant names:

• chr14-59583538-G-A
• rs11158264

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.206 AC: 8523 AN: 41466

American (AMR) AF: 0.557 AC: 8519 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1914 AN: 3464

East Asian (EAS) AF: 0.845 AC: 4370 AN: 5174

South Asian (SAS) AF: 0.569 AC: 2739 AN: 4812

European-Finnish (FIN) AF: 0.717 AC: 7580 AN: 10574

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42465 AN: 67968

Other (OTH) AF: 0.532 AC: 1124 AN: 2112

Alfa AF: 0.584 Hom.: 14088

Bravo AF: 0.488

Asia WGS AF: 0.688 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.48
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs11158264; hg19: chr14-60050256;