chr14-52077506-G-A

Variant names:

• chr14-52077506-G-A
• rs10498441

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 0.52 in 151,962 control chromosomes in the GnomAD database, including 22,942 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 0.52 (22942 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79051 AN: 151842 Hom.: 22950 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.520 AC: 79038 AN: 151962 Hom.: 22942 Cov.: 31 AF XY: 0.515 AC XY: 38249 AN XY: 74256

African (AFR) AF: 0.280 AC: 11595 AN: 41448

American (AMR) AF: 0.443 AC: 6752 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2022 AN: 3466

East Asian (EAS) AF: 0.272 AC: 1404 AN: 5160

South Asian (SAS) AF: 0.515 AC: 2478 AN: 4814

European-Finnish (FIN) AF: 0.695 AC: 7334 AN: 10546

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.670 AC: 45551 AN: 67964

Other (OTH) AF: 0.537 AC: 1133 AN: 2108

Alfa AF: 0.612 Hom.: 129811

Bravo AF: 0.488

Asia WGS AF: 0.406 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.3
DANN	Benign	0.67
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs10498441; hg19: chr14-52544224;