rs7019259

chr9-78423304-A-G

Variant summary

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

The XR_001746759.2(LOC107987083):n.1147+1112A>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 0.0835 in 152,242 control chromosomes in the GnomAD database, including 645 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 0.084 (645 hom., cov: 32)
• Consequence: LOC107987083 XR_001746759.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

Genes affected

LOC107987083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987083	XR_001746759.2	n.1147+1112A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0835 AC: 12699 AN: 152124 Hom.: 642 Cov.: 32

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0923

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0606

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.0835 AC: 12715 AN: 152242 Hom.: 645 Cov.: 32 AF XY: 0.0870 AC XY: 6476 AN XY: 74442

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.0923

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0606

Gnomad4 OTH AF: 0.0914

Alfa AF: 0.0695 Hom.: 972

Bravo AF: 0.0871

Asia WGS AF: 0.217 AC: 751 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	0.90
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7019259; hg19: chr9-81038220;