rs4266352

Positions:

• chr4-108545191-A-G

Variant summary

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

The NR_026968.1(RPL34-DT):​n.951-2975T>C 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 0.19 in 152,168 control chromosomes in the GnomAD database, including 3,633 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 0.19 (3633 hom., cov: 32)
• Consequence: RPL34-DT NR_026968.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566

Genes affected

RPL34-DT (HGNC:26749): (RPL34 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL34-DT	NR_026968.1	n.951-2975T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL34-DT	ENST00000507248.2	n.907-2975T>C		intron_variant, non_coding_transcript_variant		2
RPL34-DT	ENST00000506795.1	n.397-3599T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28989 AN: 152050 Hom.: 3633 Cov.: 32

Gnomad AFR AF: 0.0489

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.0322

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.190 AC: 28987 AN: 152168 Hom.: 3633 Cov.: 32 AF XY: 0.187 AC XY: 13927 AN XY: 74406

Gnomad4 AFR AF: 0.0488

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.0325

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.215

Alfa AF: 0.255 Hom.: 2515

Bravo AF: 0.179

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4266352; hg19: chr4-109466347;