rs1654260

chr19-20218302-G-Achr19-20218302-G-C

Variant summary

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

The XR_007067164.1(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_007067164.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

LOC105372310 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105372310	XR_007067164.1	n.11495C>T		non_coding_transcript_exon_variant	5/7
LOC105372310	XR_001754065.2	n.11495C>T		non_coding_transcript_exon_variant	5/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000593655.5	n.337+22198C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.478

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.279

Alfa AF: 0.198 Hom.: 4483

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1654260; hg19: chr19-20329111;