rs1317318

Positions:

• chr15-52840866-T-C

Variant summary

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

The XR_004837530.2(LOC107983981):​n.179+36242T>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 0.106 in 152,234 control chromosomes in the GnomAD database, including 911 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 0.11 (911 hom., cov: 32)
• Consequence: LOC107983981 XR_004837530.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.708

Genes affected

LOC107983981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107983981	XR_004837530.2	n.179+36242T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16138 AN: 152116 Hom.: 909 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0977

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.106 AC: 16171 AN: 152234 Hom.: 911 Cov.: 32 AF XY: 0.104 AC XY: 7707 AN XY: 74426

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.0977

Gnomad4 EAS AF: 0.0319

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.0437

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.0999

Alfa AF: 0.107 Hom.: 152

Bravo AF: 0.106

Asia WGS AF: 0.0960 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	14
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1317318; hg19: chr15-53133063;