rs10492923

Variant names:

• chr1-5132966-A-G
• rs10492923
• XR_946906.2:n.243+40A>G

Variant summary

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

The XR_946906.2(LOC105376682):​n.243+40A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.086 in 152,276 control chromosomes in the GnomAD database, including 924 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 0.086 (924 hom., cov: 32)
• Consequence: LOC105376682 XR_946906.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 0 publications found

Genes affected

LOC105376682 (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 (EAS) allele frequency at 95% confidence interval = 0.336 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: 0.0859 AC: 13075 AN: 152158 Hom.: 919 Cov.: 32

Gnomad AFR AF: 0.0621

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.0855

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

GnomAD4 genome AF: 0.0860 AC: 13092 AN: 152276 Hom.: 924 Cov.: 32 AF XY: 0.0911 AC XY: 6784 AN XY: 74446

African (AFR) AF: 0.0622 AC: 2584 AN: 41570

American (AMR) AF: 0.177 AC: 2711 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1805 AN: 5168

South Asian (SAS) AF: 0.171 AC: 823 AN: 4820

European-Finnish (FIN) AF: 0.0614 AC: 651 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0604 AC: 4110 AN: 68034

Other (OTH) AF: 0.0903 AC: 191 AN: 2116

Alfa AF: 0.0763 Hom.: 1005

Bravo AF: 0.0915

Asia WGS AF: 0.270 AC: 939 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	0.010
DANN	Benign	0.38
PhyloP100		-0.75

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10492923;

hg19: chr1-5193026;