rs343802

Variant names:

• chr1-110774507-G-A
• rs343802
• XR_001737801.2:n.-163C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-110774507-G-A
• chr1-110774507-G-C
• chr1-110774507-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001737801.2(LOC105378901):​n.-163C>T variant causes a upstream gene change. The variant allele was found at a frequency of 0.186 in 152,208 control chromosomes in the GnomAD database, including 3,284 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 0.19 (3284 hom., cov: 32)
• Consequence: LOC105378901 XR_001737801.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.87
• Publications: 5 publications found

Genes affected

LOC105378901 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 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: 0.187 AC: 28395 AN: 152090 Hom.: 3287 Cov.: 32

Gnomad AFR AF: 0.0589

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.186 AC: 28382 AN: 152208 Hom.: 3284 Cov.: 32 AF XY: 0.188 AC XY: 13950 AN XY: 74394

African (AFR) AF: 0.0588 AC: 2443 AN: 41550

American (AMR) AF: 0.226 AC: 3453 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1321 AN: 3472

East Asian (EAS) AF: 0.127 AC: 656 AN: 5178

South Asian (SAS) AF: 0.187 AC: 902 AN: 4824

European-Finnish (FIN) AF: 0.231 AC: 2440 AN: 10578

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16222 AN: 67990

Other (OTH) AF: 0.224 AC: 474 AN: 2116

Alfa AF: 0.203 Hom.: 1825

Bravo AF: 0.183

Asia WGS AF: 0.216 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	16
DANN	Benign	0.60
PhyloP100		3.9

Splicing

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

Other links and lift over

dbSNP: rs343802; hg19: chr1-111317129;