6-30415635-T-C

Variant summary

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

The ENST00000445710.1(MICC):​n.537+118T>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 0.13 in 380,088 control chromosomes in the GnomAD database, including 3,670 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 0.16 ( 2209 hom., cov: 32)
Exomes 𝑓: 0.11 ( 1461 hom. )

Consequence

MICC
ENST00000445710.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.608
Variant links:
Genes affected
MICC (HGNC:7092): (MHC class I polypeptide-related sequence C (pseudogene))

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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MICCENST00000445710.1 linkuse as main transcriptn.537+118T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.163
AC:
24758
AN:
152062
Hom.:
2208
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.238
Gnomad AMI
AF:
0.147
Gnomad AMR
AF:
0.107
Gnomad ASJ
AF:
0.134
Gnomad EAS
AF:
0.0318
Gnomad SAS
AF:
0.139
Gnomad FIN
AF:
0.0889
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.155
Gnomad OTH
AF:
0.154
GnomAD4 exome
AF:
0.108
AC:
24593
AN:
227908
Hom.:
1461
AF XY:
0.109
AC XY:
12933
AN XY:
118664
show subpopulations
Gnomad4 AFR exome
AF:
0.187
Gnomad4 AMR exome
AF:
0.0898
Gnomad4 ASJ exome
AF:
0.114
Gnomad4 EAS exome
AF:
0.0179
Gnomad4 SAS exome
AF:
0.111
Gnomad4 FIN exome
AF:
0.0653
Gnomad4 NFE exome
AF:
0.118
Gnomad4 OTH exome
AF:
0.115
GnomAD4 genome
AF:
0.163
AC:
24772
AN:
152180
Hom.:
2209
Cov.:
32
AF XY:
0.158
AC XY:
11752
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.238
Gnomad4 AMR
AF:
0.106
Gnomad4 ASJ
AF:
0.134
Gnomad4 EAS
AF:
0.0321
Gnomad4 SAS
AF:
0.140
Gnomad4 FIN
AF:
0.0889
Gnomad4 NFE
AF:
0.155
Gnomad4 OTH
AF:
0.152
Alfa
AF:
0.120
Hom.:
417
Bravo
AF:
0.170
Asia WGS
AF:
0.0740
AC:
256
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
7.3
DANN
Benign
0.46

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: rs9261850; hg19: chr6-30383412; API