rs9552241

Positions:

• chr13-20553430-G-C

Variant summary

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

The XR_941725.3(LOC105370103):​n.994-1181C>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 0.253 in 152,224 control chromosomes in the GnomAD database, including 6,092 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 0.25 (6092 hom., cov: 33)
• Consequence: LOC105370103 XR_941725.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

Genes affected

LOC105370103 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370103	XR_941725.3	n.994-1181C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38525 AN: 152108 Hom.: 6079 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.253 AC: 38551 AN: 152224 Hom.: 6092 Cov.: 33 AF XY: 0.264 AC XY: 19674 AN XY: 74406

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.226

Alfa AF: 0.233 Hom.: 586

Bravo AF: 0.261

Asia WGS AF: 0.579 AC: 2012 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	13
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9552241; hg19: chr13-21127569; COSMIC: COSV59173085;