chr2-46257171-C-T

Position:

• chr2-46257171-C-T

Variant summary

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

The ENST00000446949.1(RPL36AP14):​n.7G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 152,142 control chromosomes in the GnomAD database, including 34,997 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 0.68 (34980 hom., cov: 32)
  • Exomes 𝑓: 0.66 (17 hom.)
• Consequence: RPL36AP14 ENST00000446949.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.52

Genes affected

RPL36AP14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL36AP14		n.46257171C>T		intragenic_variant
LOC101926974	XR_940051.4	n.32-902C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL36AP14	ENST00000446949.1	n.7G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102682 AN: 151944 Hom.: 34963 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.664

GnomAD4 exome AF: 0.659 AC: 54 AN: 82 Hom.: 17 Cov.: 0 AF XY: 0.682 AC XY: 45 AN XY: 66

Gnomad4 AFR exome AF: 0.750

Gnomad4 ASJ exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.600

Gnomad4 NFE exome AF: 0.638

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.676 AC: 102741 AN: 152060 Hom.: 34980 Cov.: 32 AF XY: 0.670 AC XY: 49809 AN XY: 74336

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.700

Gnomad4 OTH AF: 0.666

Alfa AF: 0.692 Hom.: 48946

Bravo AF: 0.667

Asia WGS AF: 0.527 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17034876; hg19: chr2-46484310;