XR_007060527.1:n.179-4C>G

Variant names:

• chr7-130782816-C-G
• rs738134
• XR_007060527.1:n.179-4C>G

Variant summary

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

The XR_007060527.1(LOC105375508):​n.179-4C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,098 control chromosomes in the GnomAD database, including 8,205 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 0.32 (8205 hom., cov: 33)
• Consequence: LOC105375508 XR_007060527.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 12 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 (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49158 AN: 151978 Hom.: 8209 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.323 AC: 49155 AN: 152098 Hom.: 8205 Cov.: 33 AF XY: 0.326 AC XY: 24221 AN XY: 74358

African (AFR) AF: 0.267 AC: 11069 AN: 41498

American (AMR) AF: 0.394 AC: 6019 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1242 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2247 AN: 5186

South Asian (SAS) AF: 0.378 AC: 1821 AN: 4822

European-Finnish (FIN) AF: 0.303 AC: 3196 AN: 10558

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22488 AN: 67970

Other (OTH) AF: 0.317 AC: 670 AN: 2114

Alfa AF: 0.204 Hom.: 448

Bravo AF: 0.330

Asia WGS AF: 0.382 AC: 1324 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	0.86
DANN	Benign	0.50
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs738134; hg19: chr7-130467575;