rs1562398

Variant names:

• chr7-130773172-C-G
• rs1562398
• XR_007060527.1:n.179-9648C>G

Your query was ambiguous. Multiple possible variants found:

• chr7-130773172-C-G
• chr7-130773172-C-T

Variant summary

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

The XR_927976.3(LOC105375508):​n.179-9648C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 151,716 control chromosomes in the GnomAD database, including 24,311 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 0.55 (24311 hom., cov: 32)
• Consequence: LOC105375508 XR_927976.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 13 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 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: 0.548 AC: 83075 AN: 151594 Hom.: 24267 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.548 AC: 83167 AN: 151716 Hom.: 24311 Cov.: 32 AF XY: 0.551 AC XY: 40872 AN XY: 74128

African (AFR) AF: 0.754 AC: 31226 AN: 41436

American (AMR) AF: 0.564 AC: 8594 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1849 AN: 3466

East Asian (EAS) AF: 0.648 AC: 3346 AN: 5160

South Asian (SAS) AF: 0.554 AC: 2670 AN: 4822

European-Finnish (FIN) AF: 0.453 AC: 4750 AN: 10496

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28931 AN: 67792

Other (OTH) AF: 0.522 AC: 1100 AN: 2106

Alfa AF: 0.299 Hom.: 652

Bravo AF: 0.569

Asia WGS AF: 0.587 AC: 2023 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.60
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1562398; hg19: chr7-130457931;