XR_007068004.1:n.1293G>A

Variant names:

• chr22-19730621-G-A
• rs5748410
• XR_007068004.1:n.1293G>A

Variant summary

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

The XR_007068004.1(LOC105372861):​n.1293G>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 0.658 in 152,152 control chromosomes in the GnomAD database, including 33,512 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 0.66 (33512 hom., cov: 34)
• Consequence: LOC105372861 XR_007068004.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 6 publications found

Genes affected

LOC105372861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757762.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298759	ENST00000757762.1		n.84-1822G>A		intron	N/A
	ENSG00000298759	ENST00000757763.1		n.-228G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.658 AC: 100001 AN: 152034 Hom.: 33461 Cov.: 34

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.658 AC: 100108 AN: 152152 Hom.: 33512 Cov.: 34 AF XY: 0.660 AC XY: 49049 AN XY: 74370

African (AFR) AF: 0.775 AC: 32180 AN: 41520

American (AMR) AF: 0.629 AC: 9616 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1963 AN: 3472

East Asian (EAS) AF: 0.785 AC: 4057 AN: 5170

South Asian (SAS) AF: 0.574 AC: 2763 AN: 4816

European-Finnish (FIN) AF: 0.652 AC: 6895 AN: 10582

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40447 AN: 67984

Other (OTH) AF: 0.636 AC: 1344 AN: 2114

Alfa AF: 0.616 Hom.: 37252

Bravo AF: 0.662

Asia WGS AF: 0.674 AC: 2344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.61
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs5748410; hg19: chr22-19718144;