rs6931763

Variant names:

• chr6-30344155-A-C
• rs6931763
• ENST00000623385.3:c.1105-1143A>C

Variant summary

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

The ENST00000623385.3(TRIM39-RPP21):​c.1105-1143A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,142 control chromosomes in the GnomAD database, including 1,532 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 0.14 (1532 hom., cov: 31)
• Consequence: TRIM39-RPP21 ENST00000623385.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300
• Publications: 16 publications found

Genes affected

TRIM39-RPP21 (HGNC:38845): (TRIM39-RPP21 readthrough) This locus represents naturally occurring read-through transcription between the neighboring TRIM39 (tripartite motif-containing 39) and RPP21 (ribonuclease P/MRP 21kDa subunit) genes on chromosome 6. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623385.3. 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
	TRIM39-RPP21	NM_001199119.1		c.1105-1143A>C		intron	N/A	NP_001186048.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM39-RPP21	ENST00000623385.3	TSL:5	c.1105-1143A>C		intron	N/A	ENSP00000485378.1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20998 AN: 152024 Hom.: 1534 Cov.: 31

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0992

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.138 AC: 20989 AN: 152142 Hom.: 1532 Cov.: 31 AF XY: 0.139 AC XY: 10332 AN XY: 74376

African (AFR) AF: 0.131 AC: 5442 AN: 41500

American (AMR) AF: 0.126 AC: 1933 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3470

East Asian (EAS) AF: 0.143 AC: 738 AN: 5174

South Asian (SAS) AF: 0.228 AC: 1098 AN: 4826

European-Finnish (FIN) AF: 0.0992 AC: 1052 AN: 10602

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9390 AN: 67970

Other (OTH) AF: 0.163 AC: 345 AN: 2112

Alfa AF: 0.139 Hom.: 5604

Bravo AF: 0.139

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.72
PhyloP100		-0.0030

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6931763; hg19: chr6-30311932;