chr6-29976381-T-C

Variant names:

• chr6-29976381-T-C
• rs3823375
• ENST00000376800.7:n.406+864T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000376800.7(HCG9):​n.406+864T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 151,560 control chromosomes in the GnomAD database, including 6,420 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 0.30 (6420 hom., cov: 34)
• Consequence: HCG9 ENST00000376800.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• Publications: 23 publications found

Genes affected

HCG9 (HGNC:21243): (HLA complex group 9) This gene lies within the MHC class I region on chromosome 6p21.3. This gene is believed to be non-coding, but its function has not been determined. [provided by RefSeq, Jul 2009]

POLR1HASP (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG9	NR_028032.1	n.403+864T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG9	ENST00000376800.7	n.406+864T>C		intron_variant	Intron 1 of 2	1
POLR1HASP	ENST00000688495.1	n.1375A>G		non_coding_transcript_exon_variant	Exon 4 of 4
POLR1HASP	ENST00000849681.1	n.1612A>G		non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46058 AN: 151442 Hom.: 6416 Cov.: 34

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.304 AC: 46078 AN: 151560 Hom.: 6420 Cov.: 34 AF XY: 0.305 AC XY: 22554 AN XY: 74060

African (AFR) AF: 0.263 AC: 10819 AN: 41162

American (AMR) AF: 0.289 AC: 4412 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 715 AN: 3464

East Asian (EAS) AF: 0.311 AC: 1605 AN: 5154

South Asian (SAS) AF: 0.200 AC: 964 AN: 4812

European-Finnish (FIN) AF: 0.401 AC: 4212 AN: 10504

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22370 AN: 67888

Other (OTH) AF: 0.277 AC: 583 AN: 2106

Alfa AF: 0.310 Hom.: 13245

Asia WGS AF: 0.217 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.87
DANN	Benign	0.19
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs3823375; hg19: chr6-29944158;