rs4446605

Variant names:

• chr6-31205319-A-G
• rs4446605
• ENST00000755328.1:n.161+1209A>G

Variant summary

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

The ENST00000755328.1(HCG27):​n.161+1209A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,178 control chromosomes in the GnomAD database, including 1,218 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 0.12 (1218 hom., cov: 32)
• Consequence: HCG27 ENST00000755328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 14 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755328.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HCG27	ENST00000755328.1		n.161+1209A>G		intron	N/A
	HCG27	ENST00000755329.1		n.159+1209A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18399 AN: 152060 Hom.: 1216 Cov.: 32

Gnomad AFR AF: 0.0981

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.121 AC: 18420 AN: 152178 Hom.: 1218 Cov.: 32 AF XY: 0.125 AC XY: 9313 AN XY: 74400

African (AFR) AF: 0.0982 AC: 4074 AN: 41498

American (AMR) AF: 0.155 AC: 2371 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3470

East Asian (EAS) AF: 0.109 AC: 567 AN: 5182

South Asian (SAS) AF: 0.139 AC: 672 AN: 4826

European-Finnish (FIN) AF: 0.185 AC: 1963 AN: 10598

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7593 AN: 68004

Other (OTH) AF: 0.170 AC: 358 AN: 2110

Alfa AF: 0.122 Hom.: 1110

Bravo AF: 0.120

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.0
DANN	Benign	0.29
PhyloP100		0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4446605;

hg19: chr6-31173096;