rs6931763

Positions:

• chr6-30344155-A-C

Variant summary

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

The NM_001199119.1(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 NM_001199119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

Genes affected

TRIM39-RPP21 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM39-RPP21	NM_001199119.1	c.1105-1143A>C		intron_variant			NP_001186048.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.0992

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.163

Alfa AF: 0.142 Hom.: 2280

Bravo AF: 0.139

Asia WGS AF: 0.160 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs6931763; hg19: chr6-30311932;