4-80243569-C-T

Variant names:

• chr4-80243569-C-T
• rs1458038
• XR_007058161.1:n.80+11283C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007058161.1(LOC124900725):​n.80+11283C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98
• Publications: 110 publications found

Genes affected

LOC124900725 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124900725	XR_007058161.1	n.80+11283C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0825 AC: 3424 AN: 41478

American (AMR) AF: 0.257 AC: 3923 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 834 AN: 3466

East Asian (EAS) AF: 0.417 AC: 2135 AN: 5126

South Asian (SAS) AF: 0.286 AC: 1376 AN: 4818

European-Finnish (FIN) AF: 0.320 AC: 3385 AN: 10564

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

European-Non Finnish (NFE) AF: 0.296 AC: 20121 AN: 67924

Other (OTH) AF: 0.227 AC: 479 AN: 2114

Alfa AF: 0.276 Hom.: 27787

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
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs1458038; hg19: chr4-81164723;