rs10456378

Variant names:

• chr6-30238409-G-A
• rs10456378
• ENST00000427723.1:n.109G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

Genes affected

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

HCG18 (HGNC:31337): (HLA complex group 18)

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRIM26BP		n.30238409G>A		intragenic_variant
HCG17	NR_052012.1	n.409+3738C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM26BP	ENST00000427723.1	n.109G>A		non_coding_transcript_exon_variant	Exon 1 of 3	6
HCG18	ENST00000453558.2	n.662+3738C>T		intron_variant	Intron 3 of 4	5
HCG18	ENST00000844410.1	n.316+3738C>T		intron_variant	Intron 3 of 4

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0417 AC: 1 AN: 24

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.0101 AC: 419 AN: 41548

American (AMR) AF: 0.0318 AC: 486 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3468

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5168

South Asian (SAS) AF: 0.0118 AC: 57 AN: 4812

European-Finnish (FIN) AF: 0.0554 AC: 587 AN: 10588

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0525 AC: 3573 AN: 67996

Other (OTH) AF: 0.0502 AC: 106 AN: 2112

Alfa AF: 0.0467 Hom.: 682

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
PhyloP100		0.74
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10456378; hg19: chr6-30206186;