14-48691286-G-T

Variant names:

• chr14-48691286-G-T
• rs1953915
• XR_007064152.1:n.425+45103C>A

Variant summary

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

The XR_007064152.1(LOC105378178):​n.425+45103C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 151,832 control chromosomes in the GnomAD database, including 26,896 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 0.59 (26896 hom., cov: 30)
• Consequence: LOC105378178 XR_007064152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 4 publications found

Genes affected

LOC105378178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378178	XR_007064152.1	n.425+45103C>A		intron_variant	Intron 5 of 9

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89518 AN: 151714 Hom.: 26846 Cov.: 30

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.590 AC: 89630 AN: 151832 Hom.: 26896 Cov.: 30 AF XY: 0.594 AC XY: 44062 AN XY: 74186

African (AFR) AF: 0.659 AC: 27249 AN: 41378

American (AMR) AF: 0.575 AC: 8775 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2031 AN: 3466

East Asian (EAS) AF: 0.746 AC: 3837 AN: 5144

South Asian (SAS) AF: 0.689 AC: 3314 AN: 4810

European-Finnish (FIN) AF: 0.555 AC: 5836 AN: 10510

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36801 AN: 67960

Other (OTH) AF: 0.581 AC: 1221 AN: 2102

Alfa AF: 0.560 Hom.: 13259

Bravo AF: 0.588

Asia WGS AF: 0.734 AC: 2552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.73
DANN	Benign	0.21
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1953915; hg19: chr14-49160489;