XR_007061735.1:n.170G>A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902250	XR_007061735.1	n.170G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;