rs3094117

chr6-30769709-A-C

Variant summary

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

The NR_138037.1(HCG20):n.127+2758A>C 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 0.281 in 151,824 control chromosomes in the GnomAD database, including 6,193 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 0.28 (6193 hom., cov: 31)
• Consequence: HCG20 NR_138037.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG20	NR_138037.1	n.127+2758A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HCG20	ENST00000656751.1	n.86-18982A>C		intron_variant, non_coding_transcript_variant
HCG20	ENST00000439406.6	n.154+2758A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42636 AN: 151708 Hom.: 6185 Cov.: 31

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.281 AC: 42682 AN: 151824 Hom.: 6193 Cov.: 31 AF XY: 0.274 AC XY: 20347 AN XY: 74184

Gnomad4 AFR AF: 0.343

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.290

Alfa AF: 0.278 Hom.: 4800

Bravo AF: 0.293

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.4
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3094117; hg19: chr6-30737486;