1-31385151-A-G

Variant names:

• chr1-31385151-A-G
• rs10914372
• XR_947141.3:n.65-1149T>C

Variant summary

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

The XR_947141.3(LOC105378623):​n.65-1149T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,812 control chromosomes in the GnomAD database, including 3,575 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 0.20 (3575 hom., cov: 30)
• Consequence: LOC105378623 XR_947141.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 4 publications found

Genes affected

LOC105378623 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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: 0.199 AC: 30138 AN: 151696 Hom.: 3571 Cov.: 30

Gnomad AFR AF: 0.0967

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.199 AC: 30152 AN: 151812 Hom.: 3575 Cov.: 30 AF XY: 0.205 AC XY: 15176 AN XY: 74182

African (AFR) AF: 0.0966 AC: 4004 AN: 41432

American (AMR) AF: 0.267 AC: 4069 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 910 AN: 3466

East Asian (EAS) AF: 0.423 AC: 2170 AN: 5132

South Asian (SAS) AF: 0.374 AC: 1797 AN: 4802

European-Finnish (FIN) AF: 0.227 AC: 2388 AN: 10528

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

European-Non Finnish (NFE) AF: 0.207 AC: 14089 AN: 67914

Other (OTH) AF: 0.223 AC: 468 AN: 2100

Alfa AF: 0.215 Hom.: 2792

Bravo AF: 0.197

Asia WGS AF: 0.348 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.8
DANN	Benign	0.67
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs10914372; hg19: chr1-31857998; COSMIC: COSV59936024;