rs5748410

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372861	XR_007068004.1	n.1293G>A		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105372861	XR_938005.3	n.981-1822G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298759	ENST00000757762.1	n.84-1822G>A		intron_variant	Intron 1 of 2
ENSG00000298759	ENST00000757763.1	n.-228G>A		upstream_gene_variant

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 v4.3

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;