rs1317019

Positions:

• chr2-18959268-A-G

Variant summary

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

The XR_007086234.1(LOC105373456):​n.1138+39891A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 151,972 control chromosomes in the GnomAD database, including 5,918 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 0.27 (5918 hom., cov: 32)
• Consequence: LOC105373456 XR_007086234.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

LOC105373456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373456	XR_007086234.1	n.1138+39891A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41068 AN: 151854 Hom.: 5891 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.271 AC: 41144 AN: 151972 Hom.: 5918 Cov.: 32 AF XY: 0.270 AC XY: 20063 AN XY: 74294

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.294

Alfa AF: 0.230 Hom.: 5530

Bravo AF: 0.278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.011

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1317019; hg19: chr2-19140546;