14-48665087-T-G

Variant names:

• chr14-48665087-T-G
• rs10498413
• XR_007064152.1:n.425+71302A>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+71302A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,502 control chromosomes in the GnomAD database, including 11,848 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 0.39 (11848 hom., cov: 31)
• Consequence: LOC105378178 XR_007064152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 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: 0.390 AC: 58987 AN: 151384 Hom.: 11848 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.389 AC: 59004 AN: 151502 Hom.: 11848 Cov.: 31 AF XY: 0.386 AC XY: 28588 AN XY: 74028

African (AFR) AF: 0.333 AC: 13766 AN: 41382

American (AMR) AF: 0.407 AC: 6162 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1361 AN: 3464

East Asian (EAS) AF: 0.246 AC: 1269 AN: 5156

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4812

European-Finnish (FIN) AF: 0.417 AC: 4400 AN: 10554

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29250 AN: 67686

Other (OTH) AF: 0.403 AC: 847 AN: 2104

Alfa AF: 0.415 Hom.: 41323

Bravo AF: 0.393

Asia WGS AF: 0.249 AC: 864 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.1
DANN	Benign	0.83
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10498413; hg19: chr14-49134290;