3-187931631-T-C

Variant names:

• chr3-187931631-T-C
• rs6773854
• XR_924814.1:n.1283A>G

Variant summary

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

The XR_924814.1(LOC105374265):​n.1283A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,048 control chromosomes in the GnomAD database, including 4,235 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 0.23 (4235 hom., cov: 32)
• Consequence: LOC105374265 XR_924814.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 23 publications found

Genes affected

LOC105374265 (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 (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.230 AC: 34964 AN: 151928 Hom.: 4228 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.230 AC: 34990 AN: 152048 Hom.: 4235 Cov.: 32 AF XY: 0.227 AC XY: 16874 AN XY: 74318

African (AFR) AF: 0.293 AC: 12149 AN: 41468

American (AMR) AF: 0.176 AC: 2696 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1057 AN: 3472

East Asian (EAS) AF: 0.183 AC: 947 AN: 5164

South Asian (SAS) AF: 0.124 AC: 598 AN: 4826

European-Finnish (FIN) AF: 0.218 AC: 2303 AN: 10554

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14383 AN: 67966

Other (OTH) AF: 0.227 AC: 478 AN: 2108

Alfa AF: 0.216 Hom.: 15861

Bravo AF: 0.233

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.80
DANN	Benign	0.46
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs6773854; hg19: chr3-187649419;