rs1953516

chr13-20307007-G-Achr13-20307007-G-T

Variant summary

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

The XR_941720.2(LOC105370102):n.106+11214G>A 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 0.391 in 152,096 control chromosomes in the GnomAD database, including 12,708 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 0.39 (12708 hom., cov: 33)
• Consequence: LOC105370102 XR_941720.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

Genes affected

LOC105370102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370102	XR_941720.2	n.106+11214G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59487 AN: 151978 Hom.: 12705 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.391 AC: 59509 AN: 152096 Hom.: 12708 Cov.: 33 AF XY: 0.389 AC XY: 28932 AN XY: 74326

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.381

Alfa AF: 0.453 Hom.: 32554

Bravo AF: 0.380

Asia WGS AF: 0.362 AC: 1260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.1
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1953516; hg19: chr13-20881146;