rs680798

Variant names:

• chr18-34938826-A-G
• rs680798
• XR_007066333.1:n.144+4398T>C

Variant summary

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

The XR_007066333.1(LOC105372061):​n.144+4398T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,076 control chromosomes in the GnomAD database, including 7,357 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 0.29 (7357 hom., cov: 32)
• Consequence: LOC105372061 XR_007066333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 6 publications found

Genes affected

LOC105372061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.367 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: 0.294 AC: 44708 AN: 151958 Hom.: 7352 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.294 AC: 44725 AN: 152076 Hom.: 7357 Cov.: 32 AF XY: 0.295 AC XY: 21916 AN XY: 74318

African (AFR) AF: 0.146 AC: 6074 AN: 41502

American (AMR) AF: 0.337 AC: 5144 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1112 AN: 5168

South Asian (SAS) AF: 0.291 AC: 1402 AN: 4824

European-Finnish (FIN) AF: 0.354 AC: 3742 AN: 10558

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25221 AN: 67962

Other (OTH) AF: 0.308 AC: 650 AN: 2112

Alfa AF: 0.348 Hom.: 40727

Bravo AF: 0.286

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.84
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs680798; hg19: chr18-32518790;