rs10498407

chr14-48589042-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007064152.1(LOC105378178):n.425+147347G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,150 control chromosomes in the GnomAD database, including 2,929 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 0.17 (2929 hom., cov: 33)
• Consequence: LOC105378178 XR_007064152.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

Genes affected

LOC105378178 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378178	XR_007064152.1	n.425+147347G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26329 AN: 152032 Hom.: 2933 Cov.: 33

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0357

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.173 AC: 26320 AN: 152150 Hom.: 2929 Cov.: 33 AF XY: 0.167 AC XY: 12394 AN XY: 74368

Gnomad4 AFR AF: 0.0531

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0356

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.192

Alfa AF: 0.226 Hom.: 2055

Bravo AF: 0.168

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.17
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498407; hg19: chr14-49058245;