rs2844773

Positions:

• chr6-30239718-C-A

Variant summary

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

The variant allele was found at a frequency of 0.112 in 152,266 control chromosomes in the GnomAD database, including 1,140 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 0.11 (1140 hom., cov: 32)
• Consequence: TRIM26BP intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664

Genes affected

TRIM26BP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM26BP		n.30239718C>A		intragenic_variant
HCG17	NR_052012.1	n.409+2429G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM26BP	ENST00000427723.1	n.405+1013C>A		intron_variant		6
HCG17	ENST00000453558.1	n.409+2429G>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16975 AN: 152148 Hom.: 1133 Cov.: 32

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0718

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.00615

Gnomad SAS AF: 0.0593

Gnomad FIN AF: 0.0935

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.0976

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

GnomAD4 genome AF: 0.112 AC: 17010 AN: 152266 Hom.: 1140 Cov.: 32 AF XY: 0.106 AC XY: 7893 AN XY: 74452

Gnomad4 AFR AF: 0.0940

Gnomad4 AMR AF: 0.0717

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.00617

Gnomad4 SAS AF: 0.0604

Gnomad4 FIN AF: 0.0935

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.103

Alfa AF: 0.132 Hom.: 866

Bravo AF: 0.109

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2844773; hg19: chr6-30207495;