rs4452124

chr2-203934974-C-T

Variant summary

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

The XR_427213.4(LOC101927840):n.408+1134G>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 0.777 in 152,174 control chromosomes in the GnomAD database, including 49,093 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 0.78 (49093 hom., cov: 33)
• Consequence: LOC101927840 XR_427213.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734

Genes affected

LOC101927840 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927840	XR_427213.4	n.408+1134G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118253 AN: 152056 Hom.: 49091 Cov.: 33

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.926

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.777 AC: 118273 AN: 152174 Hom.: 49093 Cov.: 33 AF XY: 0.778 AC XY: 57859 AN XY: 74412

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.932

Gnomad4 NFE AF: 0.926

Gnomad4 OTH AF: 0.802

Alfa AF: 0.898 Hom.: 89312

Bravo AF: 0.754

Asia WGS AF: 0.816 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.22
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4452124; hg19: chr2-204799697;