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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370466	XR_943790.3	n.829+14206C>A		intron_variant	Intron 2 of 2
LOC105370466	XR_943792.3	n.840-4995C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;