XR_001739545.2:n.17918C>G

Variant names:

• chr2-75290784-G-C
• rs10490312
• XR_001739545.2:n.17918C>G

Variant summary

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

The XR_001739545.2(LOC107985900):​n.17918C>G 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 0.104 in 152,262 control chromosomes in the GnomAD database, including 1,022 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 0.10 (1022 hom., cov: 32)
• Consequence: LOC107985900 XR_001739545.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 2 publications found

Genes affected

LOC107985900 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985900	XR_001739545.2	n.17918C>G		non_coding_transcript_exon_variant	Exon 1 of 2
LOC107985900	XR_001739546.2	n.17918C>G		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306791	ENST00000821156.1	n.249-11537C>G		intron_variant	Intron 1 of 2
ENSG00000306791	ENST00000821157.1	n.173-15647C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15841 AN: 152144 Hom.: 1022 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.00635

Gnomad SAS AF: 0.0598

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.104 AC: 15853 AN: 152262 Hom.: 1022 Cov.: 32 AF XY: 0.101 AC XY: 7491 AN XY: 74440

African (AFR) AF: 0.0569 AC: 2363 AN: 41558

American (AMR) AF: 0.100 AC: 1529 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 395 AN: 3470

East Asian (EAS) AF: 0.00637 AC: 33 AN: 5184

South Asian (SAS) AF: 0.0603 AC: 291 AN: 4826

European-Finnish (FIN) AF: 0.0944 AC: 1001 AN: 10604

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9850 AN: 68008

Other (OTH) AF: 0.125 AC: 264 AN: 2112

Alfa AF: 0.119 Hom.: 147

Bravo AF: 0.102

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10490312; hg19: chr2-75517910;