rs10491318

Variant names:

• chr5-13545370-T-C
• rs10491318
• XR_001742606.2:n.502+31222A>G

Variant summary

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

The XR_001742606.2(LOC105374660):​n.502+31222A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,946 control chromosomes in the GnomAD database, including 4,699 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 (4699 hom., cov: 32)
• Consequence: LOC105374660 XR_001742606.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74
• Publications: 2 publications found

Genes affected

LOC105374660 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 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: 34959 AN: 151830 Hom.: 4704 Cov.: 32

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.230 AC: 34945 AN: 151946 Hom.: 4699 Cov.: 32 AF XY: 0.230 AC XY: 17113 AN XY: 74270

African (AFR) AF: 0.0970 AC: 4024 AN: 41500

American (AMR) AF: 0.190 AC: 2900 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1100 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1886 AN: 5136

South Asian (SAS) AF: 0.161 AC: 777 AN: 4822

European-Finnish (FIN) AF: 0.302 AC: 3196 AN: 10566

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

European-Non Finnish (NFE) AF: 0.298 AC: 20255 AN: 67890

Other (OTH) AF: 0.255 AC: 538 AN: 2110

Alfa AF: 0.279 Hom.: 1540

Bravo AF: 0.217

Asia WGS AF: 0.193 AC: 671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0050
DANN	Benign	0.71
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs10491318; hg19: chr5-13545479;