rs10491318

chr5-13545370-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001742606.2(LOC105374660):n.502+31222A>G variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74

Genes affected

LOC105374660 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105374660	XR_001742606.2	n.502+31222A>G		intron_variant, non_coding_transcript_variant
LOC105374660	XR_007058696.1	n.635-28904A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0970

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.255

Alfa AF: 0.282 Hom.: 1300

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491318; hg19: chr5-13545479;