rs718276

Positions:

• chr15-81643694-A-G

Variant summary

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

The XR_001751636.2(LOC102723985):​n.4836T>C 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 0.323 in 151,988 control chromosomes in the GnomAD database, including 9,497 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 0.32 (9497 hom., cov: 32)
• Consequence: LOC102723985 XR_001751636.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

Genes affected

LOC102723985 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102723985	XR_001751636.2	n.4836T>C		non_coding_transcript_exon_variant	3/4
LOC102723985	XR_007064735.1	n.19108T>C		non_coding_transcript_exon_variant	3/4
LOC102723985	XR_007064738.1	n.20079T>C		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259594	ENST00000558141.5	n.29-24474A>G		intron_variant		3
ENSG00000259543	ENST00000559211.1	n.266+33518A>G		intron_variant		4
ENSG00000259692	ENST00000559428.2	n.96-1259T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48969 AN: 151870 Hom.: 9478 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.323 AC: 49044 AN: 151988 Hom.: 9497 Cov.: 32 AF XY: 0.323 AC XY: 24024 AN XY: 74282

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.318

Alfa AF: 0.275 Hom.: 1071

Bravo AF: 0.357

Asia WGS AF: 0.404 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	1.4
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718276; hg19: chr15-81936035;