1-118841195-T-C

Variant names:

• chr1-118841195-T-C
• rs1766803
• XR_001737805.1:n.429+24679A>G

Variant summary

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

The XR_001737805.1(LOC107985447):​n.429+24679A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,854 control chromosomes in the GnomAD database, including 9,581 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 0.35 (9581 hom., cov: 31)
• Consequence: LOC107985447 XR_001737805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.779
• Publications: 7 publications found

Genes affected

LOC107985447 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 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: 0.354 AC: 53656 AN: 151736 Hom.: 9568 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.354 AC: 53692 AN: 151854 Hom.: 9581 Cov.: 31 AF XY: 0.353 AC XY: 26226 AN XY: 74216

African (AFR) AF: 0.345 AC: 14275 AN: 41386

American (AMR) AF: 0.322 AC: 4905 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1540 AN: 5152

South Asian (SAS) AF: 0.296 AC: 1423 AN: 4808

European-Finnish (FIN) AF: 0.391 AC: 4126 AN: 10550

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 25015 AN: 67940

Other (OTH) AF: 0.354 AC: 746 AN: 2110

Alfa AF: 0.362 Hom.: 40806

Bravo AF: 0.349

Asia WGS AF: 0.280 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.48
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs1766803; hg19: chr1-119383818;