6-30239718-C-A

Variant names:

• chr6-30239718-C-A
• rs2844773

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 25 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427723.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG17	NR_052012.1		n.409+2429G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM26BP	ENST00000427723.1	TSL:6	n.405+1013C>A		intron	N/A
	HCG18	ENST00000453558.2	TSL:5	n.662+2429G>T		intron	N/A
	HCG18	ENST00000844410.1		n.316+2429G>T		intron	N/A

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

African (AFR) AF: 0.0940 AC: 3904 AN: 41540

American (AMR) AF: 0.0717 AC: 1096 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3472

East Asian (EAS) AF: 0.00617 AC: 32 AN: 5188

South Asian (SAS) AF: 0.0604 AC: 292 AN: 4832

European-Finnish (FIN) AF: 0.0935 AC: 992 AN: 10610

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10052 AN: 68016

Other (OTH) AF: 0.103 AC: 217 AN: 2112

Alfa AF: 0.133 Hom.: 3396

Bravo AF: 0.109

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.66
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: rs2844773; hg19: chr6-30207495;