7-130782095-A-G

Variant names:

• chr7-130782095-A-G
• rs972283
• XR_007060527.1:n.179-725A>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.179-725A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,002 control chromosomes in the GnomAD database, including 32,010 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 0.63 (32010 hom., cov: 31)
• Consequence: LOC105375508 XR_007060527.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 166 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 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: 0.634 AC: 96226 AN: 151884 Hom.: 31971 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.634 AC: 96312 AN: 152002 Hom.: 32010 Cov.: 31 AF XY: 0.636 AC XY: 47249 AN XY: 74306

African (AFR) AF: 0.840 AC: 34858 AN: 41516

American (AMR) AF: 0.629 AC: 9616 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2156 AN: 3470

East Asian (EAS) AF: 0.699 AC: 3609 AN: 5164

South Asian (SAS) AF: 0.614 AC: 2956 AN: 4814

European-Finnish (FIN) AF: 0.556 AC: 5854 AN: 10526

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35108 AN: 67920

Other (OTH) AF: 0.616 AC: 1299 AN: 2110

Alfa AF: 0.563 Hom.: 90167

Bravo AF: 0.650

Asia WGS AF: 0.635 AC: 2207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.8
DANN	Benign	0.55
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs972283; hg19: chr7-130466854;