XR_007060489.1:n.-219A>G

Variant names:

• chr7-116810801-A-G
• rs41752
• XR_007060489.1:n.-219A>G

Variant summary

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

The XR_007060489.1(LOC124901731):​n.-219A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,128 control chromosomes in the GnomAD database, including 10,368 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 0.34 (10368 hom., cov: 32)
• Consequence: LOC124901731 XR_007060489.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 8 publications found

Genes affected

LOC124901731 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 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: 0.345 AC: 52432 AN: 152010 Hom.: 10380 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.344 AC: 52402 AN: 152128 Hom.: 10368 Cov.: 32 AF XY: 0.350 AC XY: 26004 AN XY: 74364

African (AFR) AF: 0.136 AC: 5640 AN: 41512

American (AMR) AF: 0.416 AC: 6367 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1621 AN: 3472

East Asian (EAS) AF: 0.503 AC: 2594 AN: 5162

South Asian (SAS) AF: 0.484 AC: 2333 AN: 4822

European-Finnish (FIN) AF: 0.412 AC: 4355 AN: 10576

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28212 AN: 67970

Other (OTH) AF: 0.367 AC: 774 AN: 2110

Alfa AF: 0.398 Hom.: 7053

Bravo AF: 0.336

Asia WGS AF: 0.443 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.84
DANN	Benign	0.55
PhyloP100		0.017
PromoterAI		-0.029	Neutral

Splicing

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

Other links and lift over

dbSNP: rs41752; hg19: chr7-116450855;