rs2965317

Positions:

• chr15-47969523-C-T

Variant summary

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

The XR_001751521.2(LOC102724553):​n.666G>A 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 0.847 in 151,648 control chromosomes in the GnomAD database, including 56,127 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 0.85 (56127 hom., cov: 31)
• Consequence: LOC102724553 XR_001751521.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722

Genes affected

LOC102724553 (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 (NFE) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724553	XR_001751521.2	n.666G>A		non_coding_transcript_exon_variant	3/3
LOC124900354	XR_001751516.3	n.143-23186C>T		intron_variant
LOC124900354	XR_001751517.2	n.143-23186C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.196-23186C>T		intron_variant		4
ENSG00000287439	ENST00000657831.1	n.409-8898G>A		intron_variant
ENSG00000259754	ENST00000662551.1	n.189-23186C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128433 AN: 151530 Hom.: 56118 Cov.: 31

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.961

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.847 AC: 128484 AN: 151648 Hom.: 56127 Cov.: 31 AF XY: 0.844 AC XY: 62621 AN XY: 74164

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.827

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.615

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.961

Gnomad4 OTH AF: 0.870

Alfa AF: 0.902 Hom.: 19270

Bravo AF: 0.828

Asia WGS AF: 0.697 AC: 2423 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	7.2
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2965317; hg19: chr15-48261720;