chr22-32378142-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000230736 (HGNC:):

RFPL3S (HGNC:9981): (RFPL3 antisense)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420171.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC339666	NR_038918.1		n.470+405T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230736	ENST00000420171.1	TSL:1	n.470+405T>C		intron	N/A
	RFPL3S	ENST00000577714.1	TSL:5	n.177-793A>G		intron	N/A
	RFPL3S	ENST00000655996.1		n.231-793A>G		intron	N/A

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

African (AFR) AF: 0.803 AC: 33288 AN: 41448

American (AMR) AF: 0.508 AC: 7756 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3466

East Asian (EAS) AF: 0.541 AC: 2783 AN: 5144

South Asian (SAS) AF: 0.483 AC: 2323 AN: 4814

European-Finnish (FIN) AF: 0.302 AC: 3200 AN: 10582

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25046 AN: 67950

Other (OTH) AF: 0.473 AC: 999 AN: 2110

Alfa AF: 0.397 Hom.: 19914

Bravo AF: 0.532

Asia WGS AF: 0.507 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.39
PhyloP100		-2.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2076036; hg19: chr22-32774129;