rs2965317

Variant names:

• chr15-47969523-C-T
• rs2965317
• XR_001751521.2:n.666G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

LOC102724553 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC102724553	XR_001751521.2	n.666G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC124900354	XR_001751516.3	n.143-23186C>T		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.143-23186C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.196-23186C>T		intron_variant	Intron 1 of 2	4
ENSG00000287439	ENST00000657831.2	n.442-8898G>A		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000662551.1	n.189-23186C>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.664 AC: 27204 AN: 40972

American (AMR) AF: 0.827 AC: 12634 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.946 AC: 3283 AN: 3472

East Asian (EAS) AF: 0.615 AC: 3171 AN: 5154

South Asian (SAS) AF: 0.793 AC: 3822 AN: 4820

European-Finnish (FIN) AF: 0.942 AC: 9991 AN: 10604

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.961 AC: 65402 AN: 68030

Other (OTH) AF: 0.870 AC: 1833 AN: 2106

Alfa AF: 0.899 Hom.: 24217

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
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs2965317; hg19: chr15-48261720;