rs694428

chr9-117850980-G-A

Variant summary

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

The XR_007061905.1(LOC105376244):n.5906G>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 0.153 in 151,982 control chromosomes in the GnomAD database, including 2,757 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 0.15 (2757 hom., cov: 31)
• Consequence: LOC105376244 XR_007061905.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

Genes affected

LOC105376244 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376244	XR_007061905.1	n.5906G>A		non_coding_transcript_exon_variant	8/8
LOC105376244	XR_007061906.1	n.5323G>A		non_coding_transcript_exon_variant	9/9
LOC105376244	XR_007061907.1	n.5062G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000449730.1	n.337-10370C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000697639.1	n.1053+2825G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23135 AN: 151866 Hom.: 2751 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0530

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.153 AC: 23184 AN: 151982 Hom.: 2757 Cov.: 31 AF XY: 0.154 AC XY: 11430 AN XY: 74276

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0530

Gnomad4 NFE AF: 0.0598

Gnomad4 OTH AF: 0.133

Alfa AF: 0.0798 Hom.: 1475

Bravo AF: 0.174

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.0
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs694428; hg19: chr9-120613258;