rs12498626

chr4-23475859-G-A

Variant summary

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

The XR_007058437.1(LOC105374524):n.3134-28148G>A 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 0.198 in 152,056 control chromosomes in the GnomAD database, including 3,347 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 0.20 (3347 hom., cov: 33)
• Consequence: LOC105374524 XR_007058437.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

Genes affected

LOC105374524 (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 = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374524	XR_007058437.1	n.3134-28148G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30131 AN: 151938 Hom.: 3335 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.198 AC: 30174 AN: 152056 Hom.: 3347 Cov.: 33 AF XY: 0.201 AC XY: 14954 AN XY: 74314

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.185

Alfa AF: 0.154 Hom.: 4067

Bravo AF: 0.208

Asia WGS AF: 0.273 AC: 946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.88
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12498626; hg19: chr4-23477482;