6-30788967-G-T

Variant names:

• chr6-30788967-G-T
• rs4711229
• ENST00000735942.1:n.502G>T

Variant summary

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

The ENST00000735942.1(HCG20):​n.502G>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 0.361 in 151,908 control chromosomes in the GnomAD database, including 10,905 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 0.36 (10904 hom., cov: 31)
  • Exomes 𝑓: 0.35 (1 hom.)
• Consequence: HCG20 ENST00000735942.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.223
• Publications: 14 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG20	NR_138037.1	n.309+95G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCG20	ENST00000735942.1	n.502G>T		non_coding_transcript_exon_variant	Exon 2 of 2
HCG20	ENST00000422944.1	n.351+95G>T		intron_variant	Intron 2 of 2	2
HCG20	ENST00000439406.7	n.341+95G>T		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54709 AN: 151764 Hom.: 10881 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.388

GnomAD4 exome AF: 0.346 AC: 9 AN: 26 Hom.: 1 AF XY: 0.318 AC XY: 7 AN XY: 22

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: 0.409 AC: 9 AN: 22

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.361 AC: 54775 AN: 151882 Hom.: 10904 Cov.: 31 AF XY: 0.367 AC XY: 27259 AN XY: 74214

African (AFR) AF: 0.351 AC: 14510 AN: 41384

American (AMR) AF: 0.526 AC: 8015 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2093 AN: 3466

East Asian (EAS) AF: 0.517 AC: 2672 AN: 5166

South Asian (SAS) AF: 0.654 AC: 3149 AN: 4816

European-Finnish (FIN) AF: 0.217 AC: 2290 AN: 10552

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20764 AN: 67952

Other (OTH) AF: 0.393 AC: 827 AN: 2104

Alfa AF: 0.353 Hom.: 11010

Bravo AF: 0.382

Asia WGS AF: 0.583 AC: 2031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.7
DANN	Benign	0.57
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4711229; hg19: chr6-30756744;