Variant 6-31057274-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_003948.3(HCG22):n.1701+364T>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 0.211 in 151,888 control chromosomes in the GnomAD database, including 3,736 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 0.21 ( 3736 hom., cov: 31)

Consequence

HCG22
NR_003948.3 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.194

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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HCG22	NR_003948.3 linkuse as main transcript	n.1701+364T>C		intron_variant, non_coding_transcript_variant
HCG22	NR_145427.2 linkuse as main transcript	n.1193+364T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
HCG22	ENST00000565192.1 linkuse as main transcript	n.1192+364T>C	intron_variant, non_coding_transcript_variant	2
HCG22	ENST00000426185.1 linkuse as main transcript	n.1511+364T>C	intron_variant, non_coding_transcript_variant	2
HCG22	ENST00000566475.1 linkuse as main transcript	n.300-2134T>C	intron_variant, non_coding_transcript_variant	4

Frequencies

GnomAD3 genomes

AF:

0.211

AC:

32002

AN:

151770

Hom.:

3728

Cov.:

show subpopulations

Gnomad AFR

AF:

0.276

Gnomad AMI

AF:

0.0899

Gnomad AMR

AF:

0.214

Gnomad ASJ

AF:

0.438

Gnomad EAS

AF:

0.282

Gnomad SAS

AF:

0.365

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.154

Gnomad OTH

AF:

0.246

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

GnomAD4 genome

AF:

0.211

AC:

32038

AN:

151888

Hom.:

3736

Cov.:

AF XY:

0.214

AC XY:

15876

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.276

Gnomad4 AMR

AF:

0.214

Gnomad4 ASJ

AF:

0.438

Gnomad4 EAS

AF:

0.282

Gnomad4 SAS

AF:

0.366

Gnomad4 FIN

AF:

0.136

Gnomad4 NFE

AF:

0.154

Gnomad4 OTH

AF:

0.245

Alfa

AF:

0.183

Hom.:

3827

Bravo

AF:

0.215

Asia WGS

AF:

0.338

AC:

1176

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

5.4

DANN

Benign

0.35

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