XR_001754065.2:n.11495C>T

Variant names:

• chr19-20218302-G-A
• rs1654260
• XR_001754065.2:n.11495C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001754065.2(LOC105372310):​n.11495C>T 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 0.304 in 151,776 control chromosomes in the GnomAD database, including 8,541 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 0.30 (8541 hom., cov: 31)
• Consequence: LOC105372310 XR_001754065.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 9 publications found

Genes affected

LOC105372310 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372310	XR_001754065.2	n.11495C>T		non_coding_transcript_exon_variant	Exon 5 of 6
LOC105372310	XR_007067164.1	n.11495C>T		non_coding_transcript_exon_variant	Exon 5 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267383	ENST00000585498.2	n.173+19986C>T		intron_variant	Intron 1 of 3	2
ENSG00000267383	ENST00000586657.2	n.207+19986C>T		intron_variant	Intron 1 of 2	4
ENSG00000267383	ENST00000592022.1	n.98-986C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46083 AN: 151660 Hom.: 8511 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.304 AC: 46158 AN: 151776 Hom.: 8541 Cov.: 31 AF XY: 0.307 AC XY: 22772 AN XY: 74158

African (AFR) AF: 0.500 AC: 20664 AN: 41366

American (AMR) AF: 0.314 AC: 4785 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 685 AN: 3468

East Asian (EAS) AF: 0.478 AC: 2459 AN: 5146

South Asian (SAS) AF: 0.296 AC: 1427 AN: 4820

European-Finnish (FIN) AF: 0.239 AC: 2506 AN: 10496

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12854 AN: 67924

Other (OTH) AF: 0.279 AC: 590 AN: 2112

Alfa AF: 0.227 Hom.: 17326

Bravo AF: 0.320

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.53
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1654260; hg19: chr19-20329111;