rs223993

chr4-12973922-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058047.1(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_007058047.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

Genes affected

LOC105374493 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105374493	XR_007058047.1	n.1384A>T		non_coding_transcript_exon_variant	1/3
LOC105374493	XR_007058044.1	n.1384A>T		non_coding_transcript_exon_variant	1/2
LOC105374493	XR_007058049.1	n.1384A>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0313

Gnomad4 AMR AF: 0.0940

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0917

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0413

Gnomad4 NFE AF: 0.0849

Gnomad4 OTH AF: 0.117

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223993; hg19: chr4-12975546;