rs9549447

chr13-112180926-C-T

Variant summary

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

The XR_944288.1(LOC105370370):n.2280G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,076 control chromosomes in the GnomAD database, including 12,558 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 0.37 (12558 hom., cov: 34)
• Consequence: LOC105370370 XR_944288.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139

Genes affected

LOC105370370 (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 (NFE) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370370	XR_944288.1	n.2280G>A		non_coding_transcript_exon_variant	6/6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56607 AN: 151958 Hom.: 12550 Cov.: 34

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.00405

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.372 AC: 56639 AN: 152076 Hom.: 12558 Cov.: 34 AF XY: 0.367 AC XY: 27265 AN XY: 74318

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.00425

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.395

Alfa AF: 0.477 Hom.: 36070

Bravo AF: 0.357

Asia WGS AF: 0.177 AC: 620 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	4.0
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9549447; hg19: chr13-112835240;