rs10456378

chr6-30238409-G-A

Variant summary

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

The ENST00000427723.1(TRIM26BP):n.109G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0354 in 152,236 control chromosomes in the GnomAD database, including 155 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 0.035 (155 hom., cov: 32)
  • Exomes 𝑓: 0.019 (0 hom.)
• Consequence: TRIM26BP ENST00000427723.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.740

Genes affected

TRIM26BP (HGNC:31338): (tripartite motif containing 26B, pseudogene)

HCG17 (HGNC:31339): (HLA complex group 17)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG17	NR_052012.1	n.409+3738C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM26BP	ENST00000427723.1	n.109G>A		non_coding_transcript_exon_variant	1/3
HCG17	ENST00000453558.1	n.409+3738C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0355 AC: 5392 AN: 152064 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.00999

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0507

GnomAD4 exome AF: 0.0185 AC: 1 AN: 54 Hom.: 0 Cov.: 0 AF XY: 0.0417 AC XY: 1 AN XY: 24

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0417

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0354 AC: 5393 AN: 152182 Hom.: 155 Cov.: 32 AF XY: 0.0347 AC XY: 2585 AN XY: 74414

Gnomad4 AFR AF: 0.0101

Gnomad4 AMR AF: 0.0318

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.00329

Gnomad4 SAS AF: 0.0118

Gnomad4 FIN AF: 0.0554

Gnomad4 NFE AF: 0.0525

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0490 Hom.: 293

Bravo AF: 0.0327

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.6
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10456378; hg19: chr6-30206186;