rs6903896

chr6-31200252-G-Achr6-31200252-G-C

Variant summary

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

The ENST00000606909.1(ENSG00000271821):n.430C>T variant causes a non coding transcript exon 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: ENST00000606909.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG27	NR_026791.1	n.124-2120G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000606909.1	n.430C>T		non_coding_transcript_exon_variant	2/2	5
HCG27	ENST00000383331.4	n.124-2120G>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.0789

Gnomad4 AMR AF: 0.0334

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.0880

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0159

Gnomad4 NFE AF: 0.0267

Gnomad4 OTH AF: 0.0463

Alfa AF: 0.0311 Hom.: 107

Bravo AF: 0.0483

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.3
Dann	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs6903896; hg19: chr6-31168029;