rs7586564

chr2-19588450-C-T

Variant summary

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

The XR_939780.2(LOC105373459):n.2292G>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 0.198 in 152,164 control chromosomes in the GnomAD database, including 3,247 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 0.20 (3247 hom., cov: 32)
• Consequence: LOC105373459 XR_939780.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

Genes affected

LOC105373459 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373459	XR_939780.2	n.2292G>A		non_coding_transcript_exon_variant	4/4
LOC105373459	XR_001739315.1	n.2716G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30083 AN: 152046 Hom.: 3249 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.198 AC: 30086 AN: 152164 Hom.: 3247 Cov.: 32 AF XY: 0.200 AC XY: 14851 AN XY: 74360

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.277

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.188

Alfa AF: 0.226 Hom.: 2993

Bravo AF: 0.189

Asia WGS AF: 0.172 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.1
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7586564; hg19: chr2-19788211;