XR_001746759.2:n.3871G>A

Variant names:

• chr9-78468981-G-A
• rs10125737
• XR_001746759.2:n.3871G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001746759.2(LOC107987083):​n.3871G>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 0.406 in 151,962 control chromosomes in the GnomAD database, including 13,334 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 0.41 (13334 hom., cov: 32)
• Consequence: LOC107987083 XR_001746759.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 5 publications found

Genes affected

LOC107987083 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987083	XR_001746759.2	n.3871G>A		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308267	ENST00000832902.1	n.163+18784G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61603 AN: 151844 Hom.: 13326 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.406 AC: 61639 AN: 151962 Hom.: 13334 Cov.: 32 AF XY: 0.408 AC XY: 30282 AN XY: 74258

African (AFR) AF: 0.275 AC: 11396 AN: 41458

American (AMR) AF: 0.332 AC: 5058 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3470

East Asian (EAS) AF: 0.598 AC: 3085 AN: 5160

South Asian (SAS) AF: 0.544 AC: 2617 AN: 4810

European-Finnish (FIN) AF: 0.479 AC: 5053 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31566 AN: 67946

Other (OTH) AF: 0.417 AC: 880 AN: 2112

Alfa AF: 0.444 Hom.: 58726

Bravo AF: 0.387

Asia WGS AF: 0.520 AC: 1809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.57
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10125737; hg19: chr9-81083897;