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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376682	XR_946906.2	n.243+40A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs10492923; hg19: chr1-5193026;