rs7800391

Variant names:

• chr7-110568186-C-T
• rs7800391
• XR_927864.3:n.239-3487C>T

Variant summary

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

The XR_927864.3(LOC105375452):​n.239-3487C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 151,750 control chromosomes in the GnomAD database, including 10,056 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 0.33 (10056 hom., cov: 30)
• Consequence: LOC105375452 XR_927864.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 12 publications found

Genes affected

LOC105375452 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 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: 0.328 AC: 49785 AN: 151636 Hom.: 10050 Cov.: 30

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.328 AC: 49788 AN: 151750 Hom.: 10056 Cov.: 30 AF XY: 0.330 AC XY: 24499 AN XY: 74172

African (AFR) AF: 0.0821 AC: 3400 AN: 41416

American (AMR) AF: 0.372 AC: 5660 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1323 AN: 3470

East Asian (EAS) AF: 0.546 AC: 2813 AN: 5148

South Asian (SAS) AF: 0.373 AC: 1784 AN: 4786

European-Finnish (FIN) AF: 0.408 AC: 4290 AN: 10514

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29395 AN: 67896

Other (OTH) AF: 0.327 AC: 690 AN: 2108

Alfa AF: 0.403 Hom.: 21662

Bravo AF: 0.317

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
DANN	Benign	0.69
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs7800391; hg19: chr7-110208243;