9-36419532-A-G

Variant names:

• chr9-36419532-A-G
• rs954779
• ENST00000488058.1:n.312+5081T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000488058.1(RNF38):​n.312+5081T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 152,132 control chromosomes in the GnomAD database, including 41,794 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 0.74 (41794 hom., cov: 33)
• Consequence: RNF38 ENST00000488058.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 7 publications found

Genes affected

RNF38 (HGNC:18052): (ring finger protein 38) This gene encodes a protein with a coiled-coil motif and a RING-H2 motif (C3H2C2) at its carboxy-terminus. The RING motif is a zinc-binding domain found in a large set of proteins playing roles in diverse cellular processes including oncogenesis, development, signal transduction, and apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488058.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RNF38	ENST00000488058.1	TSL:3	n.312+5081T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112548 AN: 152014 Hom.: 41731 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.741 AC: 112677 AN: 152132 Hom.: 41794 Cov.: 33 AF XY: 0.739 AC XY: 54953 AN XY: 74386

African (AFR) AF: 0.751 AC: 31163 AN: 41484

American (AMR) AF: 0.706 AC: 10795 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2372 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3490 AN: 5184

South Asian (SAS) AF: 0.745 AC: 3592 AN: 4820

European-Finnish (FIN) AF: 0.739 AC: 7814 AN: 10570

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50921 AN: 68002

Other (OTH) AF: 0.722 AC: 1526 AN: 2114

Alfa AF: 0.740 Hom.: 116647

Bravo AF: 0.735

Asia WGS AF: 0.724 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.79
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs954779; hg19: chr9-36419529;