9-117803051-G-A

Position:

• chr9-117803051-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.2899G>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 0.136 in 152,044 control chromosomes in the GnomAD database, including 1,590 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 0.14 (1588 hom., cov: 32)
  • Exomes 𝑓: 0.075 (2 hom.)
• Consequence: LOC105376244 XR_007061905.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

LOC105376244 (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 (NFE) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376244	XR_007061905.1	n.2899G>A		non_coding_transcript_exon_variant	7/8
LOC105376244	XR_007061906.1	n.2316G>A		non_coding_transcript_exon_variant	8/9
LOC105376244	XR_007061907.1	n.2146+35801G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000697639.1	n.962+16226G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20650 AN: 151820 Hom.: 1587 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.00233

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0749

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.0755 AC: 8 AN: 106 Hom.: 2 Cov.: 0 AF XY: 0.0625 AC XY: 4 AN XY: 64

Gnomad4 FIN exome AF: 0.0641

Gnomad4 NFE exome AF: 0.107

GnomAD4 genome AF: 0.136 AC: 20662 AN: 151938 Hom.: 1588 Cov.: 32 AF XY: 0.131 AC XY: 9705 AN XY: 74276

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.00233

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0749

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.151

Alfa AF: 0.137 Hom.: 790

Bravo AF: 0.138

Asia WGS AF: 0.0620 AC: 217 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	1.8
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7849955; hg19: chr9-120565329; COSMIC: COSV101414410;