rs7158872

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.290 AC: 12051 AN: 41526

American (AMR) AF: 0.521 AC: 7962 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1880 AN: 3470

East Asian (EAS) AF: 0.146 AC: 752 AN: 5148

South Asian (SAS) AF: 0.446 AC: 2152 AN: 4824

European-Finnish (FIN) AF: 0.613 AC: 6484 AN: 10582

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.588 AC: 39994 AN: 67978

Other (OTH) AF: 0.482 AC: 1018 AN: 2110

Alfa AF: 0.547 Hom.: 92432

Bravo AF: 0.467

Asia WGS AF: 0.296 AC: 1032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.50
DANN	Benign	0.52
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs7158872; hg19: chr14-49426842;