6-31200150-C-T

Variant names:

• chr6-31200150-C-T
• rs4122189
• ENST00000383331.4:n.124-2222C>T

Variant summary

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

The ENST00000383331.4(HCG27):​n.124-2222C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,150 control chromosomes in the GnomAD database, including 4,188 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 0.23 (4187 hom., cov: 32)
  • Exomes 𝑓: 0.16 (1 hom.)
• Consequence: HCG27 ENST00000383331.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• Publications: 36 publications found

Genes affected

HCG27 (HGNC:27366): (HLA complex group 27)

ENSG00000271821 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG27	NR_026791.1	n.124-2222C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG27	ENST00000383331.4	n.124-2222C>T		intron_variant	Intron 1 of 1	1
HCG27	ENST00000638546.2	n.167-2222C>T		intron_variant	Intron 1 of 1	1
HCG27	ENST00000414008.3	n.257C>T		non_coding_transcript_exon_variant	Exon 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34848 AN: 151968 Hom.: 4182 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.212

GnomAD4 exome AF: 0.156 AC: 10 AN: 64 Hom.: 1 Cov.: 0 AF XY: 0.125 AC XY: 6 AN XY: 48

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

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: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.180 AC: 9 AN: 50

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.229 AC: 34863 AN: 152086 Hom.: 4187 Cov.: 32 AF XY: 0.233 AC XY: 17327 AN XY: 74336

African (AFR) AF: 0.181 AC: 7528 AN: 41482

American (AMR) AF: 0.299 AC: 4564 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3470

East Asian (EAS) AF: 0.394 AC: 2041 AN: 5176

South Asian (SAS) AF: 0.153 AC: 740 AN: 4824

European-Finnish (FIN) AF: 0.272 AC: 2869 AN: 10566

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15562 AN: 67970

Other (OTH) AF: 0.216 AC: 456 AN: 2112

Alfa AF: 0.235 Hom.: 18533

Bravo AF: 0.231

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.72
PhyloP100		-0.88

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4122189; hg19: chr6-31167927;