6-30790689-A-G

Variant summary

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

The NR_138037.1(HCG20):n.310-200A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,992 control chromosomes in the GnomAD database, including 15,598 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 0.44 (15598 hom., cov: 31)
• Consequence: HCG20 NR_138037.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

Genes affected

HCG20 (HGNC:31334): (HLA complex group 20)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG20	NR_138037.1	n.310-200A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG20	ENST00000656751.1	n.268-200A>G		intron_variant, non_coding_transcript_variant
HCG20	ENST00000422944.1	n.352-737A>G		intron_variant, non_coding_transcript_variant		2
HCG20	ENST00000439406.6	n.337-200A>G		intron_variant, non_coding_transcript_variant		2
HCG20	ENST00000663861.1	n.443-200A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67142 AN: 151874 Hom.: 15580 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.442 AC: 67207 AN: 151992 Hom.: 15598 Cov.: 31 AF XY: 0.442 AC XY: 32859 AN XY: 74304

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.460

Alfa AF: 0.457 Hom.: 30986

Bravo AF: 0.460

Asia WGS AF: 0.597 AC: 2080 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	0.55
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: rs3131043; hg19: chr6-30758466;