rs13149993

Variant names:

• chr4-80237391-G-A
• rs13149993
• XR_007058161.1:n.80+5105G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

Genes affected

LOC124900725 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124900725	XR_007058161.1	n.80+5105G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.215 AC: 8892 AN: 41436

American (AMR) AF: 0.297 AC: 4527 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 833 AN: 3462

East Asian (EAS) AF: 0.393 AC: 2027 AN: 5162

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4820

European-Finnish (FIN) AF: 0.412 AC: 4341 AN: 10534

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21601 AN: 67900

Other (OTH) AF: 0.269 AC: 567 AN: 2108

Alfa AF: 0.296 Hom.: 8017

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
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs13149993; hg19: chr4-81158545;