rs419097

Variant names:

• chr9-111949463-C-T
• rs419097
• XR_007061735.1:n.170G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061735.1(LOC124902250):​n.170G>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 0.489 in 151,358 control chromosomes in the GnomAD database, including 18,081 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 0.49 (18081 hom., cov: 31)
• Consequence: LOC124902250 XR_007061735.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.208
• Publications: 6 publications found

Genes affected

LOC124902250 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74007 AN: 151240 Hom.: 18075 Cov.: 31

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.489 AC: 74054 AN: 151358 Hom.: 18081 Cov.: 31 AF XY: 0.487 AC XY: 36039 AN XY: 73994

African (AFR) AF: 0.490 AC: 20055 AN: 40960

American (AMR) AF: 0.494 AC: 7512 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1920 AN: 3468

East Asian (EAS) AF: 0.628 AC: 3249 AN: 5170

South Asian (SAS) AF: 0.410 AC: 1971 AN: 4810

European-Finnish (FIN) AF: 0.453 AC: 4758 AN: 10504

Middle Eastern (MID) AF: 0.452 AC: 131 AN: 290

European-Non Finnish (NFE) AF: 0.487 AC: 33112 AN: 67932

Other (OTH) AF: 0.507 AC: 1067 AN: 2104

Alfa AF: 0.491 Hom.: 78473

Bravo AF: 0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs419097; hg19: chr9-114711743;