rs1359790

chr13-80143021-G-Achr13-80143021-G-T

Variant summary

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

The XR_942116.3(LOC105370275):n.189-21145C>T 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 0.228 in 152,066 control chromosomes in the GnomAD database, including 4,398 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 0.23 (4398 hom., cov: 32)
• Consequence: LOC105370275 XR_942116.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

Genes affected

LOC105370275 (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 (AMR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370275	XR_942116.3	n.189-21145C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34607 AN: 151948 Hom.: 4393 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.228 AC: 34625 AN: 152066 Hom.: 4398 Cov.: 32 AF XY: 0.229 AC XY: 16986 AN XY: 74310

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.237

Alfa AF: 0.270 Hom.: 6807

Bravo AF: 0.231

Asia WGS AF: 0.208 AC: 724 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	1.7
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1359790; hg19: chr13-80717156;