6-30415635-T-C

Position:

• chr6-30415635-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608

Genes affected

MICC (HGNC:7092): (MHC class I polypeptide-related sequence C (pseudogene))

ACMG classification

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
MICC	ENST00000445710.1	n.537+118T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24758 AN: 152062 Hom.: 2208 Cov.: 32

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

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

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

Other links and lift over

dbSNP: rs9261850; hg19: chr6-30383412;