rs13149993

Positions:

• chr4-80237391-G-A
• chr4-80237391-G-C
• chr4-80237391-G-T

Variant summary

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

The XR_007058161.1(LOC124900725):​n.80+5105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,884 control chromosomes in the GnomAD database, including 6,835 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 0.29 (6835 hom., cov: 32)
• Consequence: LOC124900725 XR_007058161.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

Genes affected

LOC124900725 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900725	XR_007058161.1	n.80+5105G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44452 AN: 151766 Hom.: 6829 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.293 AC: 44470 AN: 151884 Hom.: 6835 Cov.: 32 AF XY: 0.295 AC XY: 21907 AN XY: 74206

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.269

Alfa AF: 0.295 Hom.: 6777

Bravo AF: 0.280

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13149993; hg19: chr4-81158545;