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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374660	XR_001742606.2	n.502+31222A>G		intron_variant	Intron 3 of 3
LOC105374660	XR_007058696.1	n.635-28904A>G		intron_variant	Intron 3 of 4

Ensembl

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

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 v4.3

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;