XR_007064152.1:n.345+112153C>A

Variant names:

• chr14-48957639-G-T
• rs7158872
• XR_007064152.1:n.345+112153C>A

Variant summary

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

The XR_007064152.1(LOC105378178):​n.345+112153C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 152,134 control chromosomes in the GnomAD database, including 19,227 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 0.48 (19227 hom., cov: 33)
• Consequence: LOC105378178 XR_007064152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

Genes affected

LOC105378178 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378178	XR_007064152.1	n.345+112153C>A		intron_variant	Intron 4 of 9

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73055 AN: 152016 Hom.: 19227 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.480 AC: 73063 AN: 152134 Hom.: 19227 Cov.: 33 AF XY: 0.480 AC XY: 35716 AN XY: 74374

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.542

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.482

Alfa AF: 0.562 Hom.: 39441

Bravo AF: 0.467

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7158872; hg19: chr14-49426842;