rs10507342

chr13-25045592-T-C

Variant summary

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

The XR_941760.4(LOC105370119):n.1853+94A>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 0.0215 in 152,324 control chromosomes in the GnomAD database, including 195 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 0.021 (195 hom., cov: 33)
• Consequence: LOC105370119 XR_941760.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

Genes affected

LOC105370119 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370119	XR_941760.4	n.1853+94A>G		intron_variant, non_coding_transcript_variant
LOC105370119	XR_001749796.2	n.1788+94A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0215 AC: 3269 AN: 152206 Hom.: 195 Cov.: 33

Gnomad AFR AF: 0.00485

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.00835

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0162

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

GnomAD4 genome AF: 0.0215 AC: 3268 AN: 152324 Hom.: 195 Cov.: 33 AF XY: 0.0247 AC XY: 1836 AN XY: 74472

Gnomad4 AFR AF: 0.00483

Gnomad4 AMR AF: 0.0261

Gnomad4 ASJ AF: 0.00835

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.0561

Gnomad4 FIN AF: 0.0362

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.0165

Alfa AF: 0.0130 Hom.: 5

Bravo AF: 0.0210

Asia WGS AF: 0.132 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	4.3
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507342; hg19: chr13-25619730;