14-48588607-T-G

Variant names:

• chr14-48588607-T-G
• rs10498406
• XR_007064152.1:n.425+147782A>C

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+147782A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,196 control chromosomes in the GnomAD database, including 8,292 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 0.31 (8292 hom., cov: 33)
• Consequence: LOC105378178 XR_007064152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.631
• Publications: 0 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 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: 0.311 AC: 47291 AN: 152078 Hom.: 8287 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.311 AC: 47323 AN: 152196 Hom.: 8292 Cov.: 33 AF XY: 0.313 AC XY: 23262 AN XY: 74386

African (AFR) AF: 0.147 AC: 6125 AN: 41548

American (AMR) AF: 0.347 AC: 5298 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1151 AN: 3470

East Asian (EAS) AF: 0.509 AC: 2636 AN: 5180

South Asian (SAS) AF: 0.464 AC: 2238 AN: 4824

European-Finnish (FIN) AF: 0.311 AC: 3290 AN: 10564

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.373 AC: 25398 AN: 68010

Other (OTH) AF: 0.328 AC: 693 AN: 2112

Alfa AF: 0.357 Hom.: 15538

Bravo AF: 0.305

Asia WGS AF: 0.492 AC: 1710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.74
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs10498406; hg19: chr14-49057810;