rs2428514

chr6-31059739-G-Achr6-31059739-G-T

Variant summary

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

The NR_003948.3(HCG22):n.2033G>A 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 0.171 in 151,884 control chromosomes in the GnomAD database, including 2,555 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 0.17 (2555 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HCG22 NR_003948.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

Genes affected

HCG22 (HGNC:27780): (HLA complex group 22 (non-protein coding)) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG22	NR_003948.3	n.2033G>A		non_coding_transcript_exon_variant	4/4
HCG22	NR_145427.2	n.1525G>A		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG22	ENST00000565192.1	n.1524G>A		non_coding_transcript_exon_variant	4/4	2
HCG22	ENST00000426185.1	n.1843G>A		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26012 AN: 151766 Hom.: 2549 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.0666

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.201

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.171 AC: 26042 AN: 151884 Hom.: 2555 Cov.: 31 AF XY: 0.171 AC XY: 12700 AN XY: 74236

Gnomad4 AFR AF: 0.253

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.0667

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.200

Alfa AF: 0.136 Hom.: 2607

Bravo AF: 0.178

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.0
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2428514; hg19: chr6-31027516;