rs4692256

chr4-27743096-C-T

Variant summary

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

The XR_925519.3(LOC105374549):n.332-2325C>T 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 0.615 in 151,486 control chromosomes in the GnomAD database, including 29,177 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 0.61 (29177 hom., cov: 31)
• Consequence: LOC105374549 XR_925519.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

Genes affected

LOC105374549 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374549	XR_925519.3	n.332-2325C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93014 AN: 151368 Hom.: 29144 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.615 AC: 93112 AN: 151486 Hom.: 29177 Cov.: 31 AF XY: 0.615 AC XY: 45493 AN XY: 74022

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.594

Alfa AF: 0.553 Hom.: 49315

Bravo AF: 0.618

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4692256; hg19: chr4-27744718;