chr9-119889620-T-G

Position:

• chr9-119889620-T-G

Variant summary

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

The XR_001746919.2(LOC107987122):​n.453-14935A>C 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 0.116 in 151,876 control chromosomes in the GnomAD database, including 1,195 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 0.12 (1195 hom., cov: 31)
• Consequence: LOC107987122 XR_001746919.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

Genes affected

LOC107987122 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107987122	XR_001746919.2	n.453-14935A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17543 AN: 151758 Hom.: 1190 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.0202

Gnomad FIN AF: 0.0668

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.116 AC: 17564 AN: 151876 Hom.: 1195 Cov.: 31 AF XY: 0.110 AC XY: 8192 AN XY: 74218

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0487

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0204

Gnomad4 FIN AF: 0.0668

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0654 Hom.: 80

Bravo AF: 0.123

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10984758; hg19: chr9-122651898; COSMIC: COSV60400292;