6-31058212-C-T

Variant summary

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

The ENST00000646461.3(HCG22):​c.*121-1196C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 151,988 control chromosomes in the GnomAD database, including 3,933 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 0.23 ( 3933 hom., cov: 31)

Consequence

HCG22
ENST00000646461.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0200
Variant links:
Genes affected

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=-0.87).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HCG22NR_003948.3 linkuse as main transcriptn.1702-1196C>T intron_variant
HCG22NR_145427.2 linkuse as main transcriptn.1194-1196C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HCG22ENST00000646461.3 linkuse as main transcriptc.*121-1196C>T intron_variant A0A8V8T945
HCG22ENST00000426185.1 linkuse as main transcriptn.1512-1196C>T intron_variant 2
HCG22ENST00000565192.1 linkuse as main transcriptn.1193-1196C>T intron_variant 2
HCG22ENST00000566475.1 linkuse as main transcriptn.300-1196C>T intron_variant 4

Frequencies

GnomAD3 genomes
AF:
0.226
AC:
34344
AN:
151870
Hom.:
3935
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.195
Gnomad AMI
AF:
0.299
Gnomad AMR
AF:
0.258
Gnomad ASJ
AF:
0.202
Gnomad EAS
AF:
0.191
Gnomad SAS
AF:
0.220
Gnomad FIN
AF:
0.292
Gnomad MID
AF:
0.291
Gnomad NFE
AF:
0.230
Gnomad OTH
AF:
0.243
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.226
AC:
34345
AN:
151988
Hom.:
3933
Cov.:
31
AF XY:
0.227
AC XY:
16862
AN XY:
74288
show subpopulations
Gnomad4 AFR
AF:
0.195
Gnomad4 AMR
AF:
0.257
Gnomad4 ASJ
AF:
0.202
Gnomad4 EAS
AF:
0.191
Gnomad4 SAS
AF:
0.219
Gnomad4 FIN
AF:
0.292
Gnomad4 NFE
AF:
0.230
Gnomad4 OTH
AF:
0.241
Alfa
AF:
0.226
Hom.:
6353
Bravo
AF:
0.223
Asia WGS
AF:
0.176
AC:
613
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
5.9
DANN
Benign
0.84

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.

Other links and lift over

dbSNP: rs9262638; hg19: chr6-31025989; API