6-31200252-G-A

Variant names:

• chr6-31200252-G-A
• rs6903896
• ENST00000383331.4:n.124-2120G>A

Variant summary

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

The ENST00000383331.4(HCG27):​n.124-2120G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.046 in 152,264 control chromosomes in the GnomAD database, including 248 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 0.046 (248 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HCG27 ENST00000383331.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 21 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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000383331.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG27	NR_026791.1		n.124-2120G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG27	ENST00000383331.4	TSL:1	n.124-2120G>A		intron	N/A
	HCG27	ENST00000638546.2	TSL:1	n.167-2120G>A		intron	N/A
	HCG27	ENST00000414008.3	TSL:4	n.359G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 6987 AN: 152146 Hom.: 247 Cov.: 32

Gnomad AFR AF: 0.0788

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0334

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0267

Gnomad OTH AF: 0.0468

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 32 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 30

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0460 AC: 6999 AN: 152264 Hom.: 248 Cov.: 32 AF XY: 0.0464 AC XY: 3457 AN XY: 74458

African (AFR) AF: 0.0789 AC: 3278 AN: 41540

American (AMR) AF: 0.0334 AC: 511 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0225 AC: 78 AN: 3470

East Asian (EAS) AF: 0.0880 AC: 456 AN: 5184

South Asian (SAS) AF: 0.116 AC: 557 AN: 4814

European-Finnish (FIN) AF: 0.0159 AC: 169 AN: 10612

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0267 AC: 1817 AN: 68018

Other (OTH) AF: 0.0463 AC: 98 AN: 2116

Alfa AF: 0.0336 Hom.: 369

Bravo AF: 0.0483

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		-0.082

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: rs6903896; hg19: chr6-31168029;