XR_001738551.1:n.23A>G

Variant names:

• chr1-236983079-A-G
• rs1625040
• XR_001738551.1:n.23A>G

Variant summary

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

The XR_001738551.1(LOC107985368):​n.23A>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 0.846 in 152,246 control chromosomes in the GnomAD database, including 54,685 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 0.85 (54685 hom., cov: 33)
• Consequence: LOC107985368 XR_001738551.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 1 publications found

Genes affected

LOC107985368 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985368	XR_001738551.1	n.23A>G		non_coding_transcript_exon_variant	Exon 1 of 3
LOC124904563	XR_007066964.1	n.*99A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302268	ENST00000785366.1	n.336+656A>G		intron_variant	Intron 2 of 2
ENSG00000302268	ENST00000785367.1	n.210+656A>G		intron_variant	Intron 2 of 2
ENSG00000302268	ENST00000785368.1	n.151+656A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128686 AN: 152126 Hom.: 54622 Cov.: 33

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.846 AC: 128809 AN: 152246 Hom.: 54685 Cov.: 33 AF XY: 0.850 AC XY: 63259 AN XY: 74428

African (AFR) AF: 0.797 AC: 33094 AN: 41536

American (AMR) AF: 0.856 AC: 13096 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2687 AN: 3472

East Asian (EAS) AF: 0.984 AC: 5077 AN: 5162

South Asian (SAS) AF: 0.898 AC: 4333 AN: 4824

European-Finnish (FIN) AF: 0.928 AC: 9850 AN: 10616

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.853 AC: 58033 AN: 68014

Other (OTH) AF: 0.807 AC: 1705 AN: 2114

Alfa AF: 0.854 Hom.: 6913

Bravo AF: 0.839

Asia WGS AF: 0.910 AC: 3167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.5
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: rs1625040; hg19: chr1-237146379;