rs7859491

chr9-119877010-T-C

Variant summary

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

The XR_001746919.2(LOC107987122):n.453-2325A>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 0.256 in 151,952 control chromosomes in the GnomAD database, including 10,086 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 0.26 (10086 hom., cov: 32)
• Consequence: LOC107987122 XR_001746919.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465

Genes affected

LOC107987122 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987122	XR_001746919.2	n.453-2325A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38824 AN: 151834 Hom.: 10042 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.256 AC: 38928 AN: 151952 Hom.: 10086 Cov.: 32 AF XY: 0.246 AC XY: 18259 AN XY: 74304

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.0671

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.208

Alfa AF: 0.242 Hom.: 1606

Bravo AF: 0.283

Asia WGS AF: 0.0700 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.0
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7859491; hg19: chr9-122639288; COSMIC: COSV60400101;