chr7-130752930-G-A

Variant names:

• chr7-130752930-G-A
• rs13233731
• XR_007060527.1:n.178+14940G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007060527.1(LOC105375508):​n.178+14940G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,912 control chromosomes in the GnomAD database, including 13,006 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 0.40 (13006 hom., cov: 31)
• Consequence: LOC105375508 XR_007060527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.688
• Publications: 40 publications found

Genes affected

LOC105375508 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61018 AN: 151794 Hom.: 13002 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.402 AC: 61035 AN: 151912 Hom.: 13006 Cov.: 31 AF XY: 0.398 AC XY: 29573 AN XY: 74246

African (AFR) AF: 0.272 AC: 11277 AN: 41430

American (AMR) AF: 0.388 AC: 5917 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1587 AN: 5164

South Asian (SAS) AF: 0.386 AC: 1851 AN: 4800

European-Finnish (FIN) AF: 0.449 AC: 4736 AN: 10550

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33103 AN: 67922

Other (OTH) AF: 0.422 AC: 892 AN: 2112

Alfa AF: 0.438 Hom.: 2651

Bravo AF: 0.391

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.42
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs13233731; hg19: chr7-130437689;