rs261946

Variant summary

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

The ENST00000602319.1(HCG18):​n.559T>C 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 0.196 in 152,186 control chromosomes in the GnomAD database, including 3,626 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 0.20 ( 3626 hom., cov: 31)
Exomes 𝑓: 0.17 ( 0 hom. )

Consequence

HCG18
ENST00000602319.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08
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=-0.92).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HCG18NR_024052.2 linkuse as main transcriptn.1018-7320T>C intron_variant
HCG18NR_024053.2 linkuse as main transcriptn.804-7320T>C intron_variant
HCG17NR_052012.1 linkuse as main transcriptn.126+22452T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HCG18ENST00000426882.6 linkuse as main transcriptn.798-7320T>C intron_variant 1
HCG18ENST00000602319.1 linkuse as main transcriptn.559T>C non_coding_transcript_exon_variant 1/16
HCG18ENST00000412685.9 linkuse as main transcriptn.509-7320T>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.196
AC:
29758
AN:
152062
Hom.:
3625
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0572
Gnomad AMI
AF:
0.300
Gnomad AMR
AF:
0.197
Gnomad ASJ
AF:
0.142
Gnomad EAS
AF:
0.275
Gnomad SAS
AF:
0.108
Gnomad FIN
AF:
0.351
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.259
Gnomad OTH
AF:
0.155
GnomAD4 exome
AF:
0.167
AC:
1
AN:
6
Hom.:
0
Cov.:
0
AF XY:
0.250
AC XY:
1
AN XY:
4
show subpopulations
Gnomad4 NFE exome
AF:
0.167
GnomAD4 genome
AF:
0.196
AC:
29770
AN:
152180
Hom.:
3626
Cov.:
31
AF XY:
0.199
AC XY:
14781
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.0573
Gnomad4 AMR
AF:
0.197
Gnomad4 ASJ
AF:
0.142
Gnomad4 EAS
AF:
0.275
Gnomad4 SAS
AF:
0.108
Gnomad4 FIN
AF:
0.351
Gnomad4 NFE
AF:
0.259
Gnomad4 OTH
AF:
0.154
Alfa
AF:
0.235
Hom.:
4648
Bravo
AF:
0.179
Asia WGS
AF:
0.152
AC:
528
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
3.2
DANN
Benign
0.59

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: rs261946; hg19: chr6-30271334; API