XR_007088092.1:n.-247T>C

Variant names:

• chr2-219061446-T-C
• rs437512
• XR_007088092.1:n.-247T>C

Variant summary

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

The XR_007088092.1(LOC124906120):​n.-247T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,312 control chromosomes in the GnomAD database, including 49,093 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 0.79 (49093 hom., cov: 36)
• Consequence: LOC124906120 XR_007088092.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12
• Publications: 3 publications found

Genes affected

LOC124906120 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 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: 0.795 AC: 120978 AN: 152194 Hom.: 49060 Cov.: 36

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.795 AC: 121059 AN: 152312 Hom.: 49093 Cov.: 36 AF XY: 0.792 AC XY: 58990 AN XY: 74472

African (AFR) AF: 0.931 AC: 38728 AN: 41582

American (AMR) AF: 0.680 AC: 10400 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2554 AN: 3472

East Asian (EAS) AF: 0.445 AC: 2304 AN: 5178

South Asian (SAS) AF: 0.727 AC: 3511 AN: 4830

European-Finnish (FIN) AF: 0.821 AC: 8701 AN: 10604

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52481 AN: 68022

Other (OTH) AF: 0.751 AC: 1588 AN: 2114

Alfa AF: 0.773 Hom.: 64059

Bravo AF: 0.787

Asia WGS AF: 0.557 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.60
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs437512; hg19: chr2-219926168;