rs1002095

Variant names:

• chr9-127783671-G-A
• rs1002095
• XR_001746946.2:n.1392-1088G>A

Variant summary

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

The XR_001746946.2(LOC107987132):​n.1392-1088G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,028 control chromosomes in the GnomAD database, including 9,370 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 0.32 (9370 hom., cov: 32)
• Consequence: LOC107987132 XR_001746946.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 13 publications found

Genes affected

LOC107987132 (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 (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987132	XR_001746946.2	n.1392-1088G>A		intron_variant	Intron 1 of 1
LOC107987132	XR_001746947.2	n.137-1088G>A		intron_variant	Intron 1 of 1
LOC107987132	XR_001746948.2	n.962-1088G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300930	ENST00000775132.1	n.-133G>A		upstream_gene_variant
ENSG00000300930	ENST00000775133.1	n.-150G>A		upstream_gene_variant
ENSG00000300930	ENST00000775134.1	n.-148G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49203 AN: 151910 Hom.: 9374 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.324 AC: 49198 AN: 152028 Hom.: 9370 Cov.: 32 AF XY: 0.320 AC XY: 23808 AN XY: 74312

African (AFR) AF: 0.121 AC: 5014 AN: 41474

American (AMR) AF: 0.403 AC: 6164 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3468

East Asian (EAS) AF: 0.589 AC: 3053 AN: 5182

South Asian (SAS) AF: 0.339 AC: 1630 AN: 4802

European-Finnish (FIN) AF: 0.304 AC: 3208 AN: 10566

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27510 AN: 67942

Other (OTH) AF: 0.349 AC: 737 AN: 2110

Alfa AF: 0.386 Hom.: 14167

Bravo AF: 0.327

Asia WGS AF: 0.408 AC: 1423 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	4.7
DANN	Benign	0.72
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs1002095; hg19: chr9-130545950;