rs1458038

Positions:

• chr4-80243569-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007058161.1(LOC124900725):​n.80+11283C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,970 control chromosomes in the GnomAD database, including 5,162 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 0.24 (5162 hom., cov: 31)
• Consequence: LOC124900725 XR_007058161.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98

Genes affected

LOC124900725 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900725	XR_007058161.1	n.80+11283C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36126 AN: 151852 Hom.: 5161 Cov.: 31

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.238 AC: 36125 AN: 151970 Hom.: 5162 Cov.: 31 AF XY: 0.240 AC XY: 17797 AN XY: 74268

Gnomad4 AFR AF: 0.0825

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.227

Alfa AF: 0.280 Hom.: 13710

Bravo AF: 0.227

Asia WGS AF: 0.323 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	18
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458038; hg19: chr4-81164723;