22-32378142-T-C

Variant names:

• chr22-32378142-T-C
• rs2076036
• ENST00000420171.1:n.470+405T>C

Variant summary

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

The ENST00000420171.1(ENSG00000230736):​n.470+405T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 152,002 control chromosomes in the GnomAD database, including 22,434 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 0.51 (22434 hom., cov: 32)
• Consequence: ENSG00000230736 ENST00000420171.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

Genes affected

ENSG00000230736 (HGNC:):

RFPL3S (HGNC:9981): (RFPL3 antisense)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC339666	NR_038918.1	n.470+405T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230736	ENST00000420171.1	n.470+405T>C		intron_variant	Intron 2 of 2	1
RFPL3S	ENST00000577714.1	n.177-793A>G		intron_variant	Intron 2 of 6	5
RFPL3S	ENST00000655996.1	n.231-793A>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes AF: 0.507 AC: 77034 AN: 151884 Hom.: 22389 Cov.: 32

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.507 AC: 77137 AN: 152002 Hom.: 22434 Cov.: 32 AF XY: 0.505 AC XY: 37527 AN XY: 74308

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.473

Alfa AF: 0.394 Hom.: 16397

Bravo AF: 0.532

Asia WGS AF: 0.507 AC: 1764 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	0.25
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2076036; hg19: chr22-32774129;