XR_007066375.1:n.66+45771A>G

Variant names:

• chr18-53697614-T-C
• rs1865555
• XR_007066375.1:n.66+45771A>G

Variant summary

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

The XR_007066375.1(LOC124904304):​n.66+45771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,070 control chromosomes in the GnomAD database, including 38,827 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 0.71 (38827 hom., cov: 32)
• Consequence: LOC124904304 XR_007066375.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 4 publications found

Genes affected

LOC124904304 (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 (SAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108260 AN: 151952 Hom.: 38798 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.880

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.712 AC: 108337 AN: 152070 Hom.: 38827 Cov.: 32 AF XY: 0.717 AC XY: 53285 AN XY: 74322

African (AFR) AF: 0.671 AC: 27849 AN: 41482

American (AMR) AF: 0.712 AC: 10871 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2459 AN: 3470

East Asian (EAS) AF: 0.583 AC: 3020 AN: 5182

South Asian (SAS) AF: 0.880 AC: 4238 AN: 4816

European-Finnish (FIN) AF: 0.814 AC: 8592 AN: 10554

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.719 AC: 48910 AN: 67986

Other (OTH) AF: 0.699 AC: 1477 AN: 2114

Alfa AF: 0.711 Hom.: 45404

Bravo AF: 0.700

Asia WGS AF: 0.714 AC: 2475 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.79
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1865555; hg19: chr18-51223984;