14-40598157-G-T

Variant names:

• chr14-40598157-G-T
• rs1953502
• XR_943790.3:n.829+14206C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_943790.3(LOC105370466):​n.829+14206C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,830 control chromosomes in the GnomAD database, including 17,793 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 0.47 (17793 hom., cov: 32)
• Consequence: LOC105370466 XR_943790.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 1 publications found

Genes affected

LOC105370466 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71433 AN: 151712 Hom.: 17777 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.471 AC: 71501 AN: 151830 Hom.: 17793 Cov.: 32 AF XY: 0.475 AC XY: 35214 AN XY: 74174

African (AFR) AF: 0.642 AC: 26615 AN: 41454

American (AMR) AF: 0.459 AC: 6994 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1565 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2768 AN: 5148

South Asian (SAS) AF: 0.512 AC: 2472 AN: 4826

European-Finnish (FIN) AF: 0.391 AC: 4110 AN: 10522

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25469 AN: 67848

Other (OTH) AF: 0.454 AC: 957 AN: 2110

Alfa AF: 0.288 Hom.: 751

Bravo AF: 0.484

Asia WGS AF: 0.529 AC: 1838 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.7
DANN	Benign	0.52
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs1953502; hg19: chr14-41067362;