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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378178	XR_007064152.1	n.425+147782A>C		intron_variant	Intron 5 of 9

Ensembl

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

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 v4.3

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;