XR_007058044.1:n.1384A>T

Variant names:

• chr4-12973922-T-A
• rs223993
• XR_007058044.1:n.1384A>T

Variant summary

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

The XR_007058044.1(LOC105374493):​n.1384A>T 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 0.0702 in 152,188 control chromosomes in the GnomAD database, including 482 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 0.070 (482 hom., cov: 32)
• Consequence: LOC105374493 XR_007058044.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 1 publications found

Genes affected

LOC105374493 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374493	XR_007058044.1	n.1384A>T		non_coding_transcript_exon_variant	Exon 1 of 2
LOC105374493	XR_007058047.1	n.1384A>T		non_coding_transcript_exon_variant	Exon 1 of 3
LOC105374493	XR_007058049.1	n.1384A>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302819	ENST00000789801.1	n.53-873A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0703 AC: 10688 AN: 152070 Hom.: 482 Cov.: 32

Gnomad AFR AF: 0.0313

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0939

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0917

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0413

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.0702 AC: 10689 AN: 152188 Hom.: 482 Cov.: 32 AF XY: 0.0706 AC XY: 5252 AN XY: 74398

African (AFR) AF: 0.0313 AC: 1297 AN: 41490

American (AMR) AF: 0.0940 AC: 1438 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 466 AN: 3470

East Asian (EAS) AF: 0.0917 AC: 474 AN: 5170

South Asian (SAS) AF: 0.105 AC: 505 AN: 4826

European-Finnish (FIN) AF: 0.0413 AC: 439 AN: 10620

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0849 AC: 5770 AN: 68000

Other (OTH) AF: 0.117 AC: 247 AN: 2114

Alfa AF: 0.0699 Hom.: 56

Bravo AF: 0.0717

Asia WGS AF: 0.0820 AC: 284 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.37
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs223993; hg19: chr4-12975546;