dbSNP rs9262632: HCG22:c.*120+121A>G (chr6-31057031-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000646461.3(HCG22):c.*120+121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 152,534 control chromosomes in the GnomAD database, including 398 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 0.064 ( 394 hom., cov: 32)

Exomes 𝑓: 0.097 ( 4 hom. )

Consequence

HCG22
ENST00000646461.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Variant links:

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]

HCG22 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCG22	NR_003948.3 link	n.1701+121A>G		intron_variant	Intron 3 of 3
HCG22	NR_145427.2 link	n.1193+121A>G		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	UniProt
HCG22	ENST00000646461.3 link	c.*120+121A>G	intron_variant	Intron 3 of 3		A0A8V8T945
HCG22	ENST00000426185.1 link	n.1511+121A>G	intron_variant	Intron 2 of 2	2
HCG22	ENST00000565192.1 link	n.1192+121A>G	intron_variant	Intron 3 of 3	2
HCG22	ENST00000566475.1 link	n.300-2377A>G	intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes

AF:

0.0636

AC:

9684

AN:

152168

Hom.:

393

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0428

Gnomad AMI

AF:

0.0363

Gnomad AMR

AF:

0.0797

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.0565

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0531

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0610

Gnomad OTH

AF:

0.0900

GnomAD4 exome

AF:

0.0968

AC:

AN:

248

Hom.:

AF XY:

0.0759

AC XY:

AN XY:

158

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0500

Gnomad4 NFE exome

AF:

0.125

Gnomad4 OTH exome

AF:

0.0278

GnomAD4 genome

AF:

0.0636

AC:

9685

AN:

152286

Hom.:

394

Cov.:

AF XY:

0.0653

AC XY:

4865

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.0429

Gnomad4 AMR

AF:

0.0796

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.0567

Gnomad4 SAS

AF:

0.122

Gnomad4 FIN

AF:

0.0531

Gnomad4 NFE

AF:

0.0610

Gnomad4 OTH

AF:

0.0905

Alfa

AF:

0.0723

Hom.:

711

Bravo

AF:

0.0639

Asia WGS

AF:

0.120

AC:

416

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.21

DANN

Benign

0.27

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over