rs285031

chr13-98133777-C-G

Variant summary

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

The XR_931670.4(LOC105370328):n.72+10062G>C 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 0.155 in 152,238 control chromosomes in the GnomAD database, including 2,016 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 0.16 (2016 hom., cov: 32)
• Consequence: LOC105370328 XR_931670.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

Genes affected

LOC105370328 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370328	XR_931670.4	n.72+10062G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23598 AN: 152120 Hom.: 2016 Cov.: 32

Gnomad AFR AF: 0.0981

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0664

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.155 AC: 23617 AN: 152238 Hom.: 2016 Cov.: 32 AF XY: 0.157 AC XY: 11649 AN XY: 74432

Gnomad4 AFR AF: 0.0980

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0663

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.161

Alfa AF: 0.161 Hom.: 251

Bravo AF: 0.156

Asia WGS AF: 0.0930 AC: 326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.9
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285031; hg19: chr13-98786031;