chr6-30416022-G-A

Position:

• chr6-30416022-G-A

Variant summary

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

The ENST00000445710.1(MICC):​n.538-97G>A 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 0.163 in 152,734 control chromosomes in the GnomAD database, including 2,213 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 (2206 hom., cov: 33)
  • Exomes 𝑓: 0.11 (7 hom.)
• Consequence: MICC ENST00000445710.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.959

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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MICC	ENST00000445710.1	n.538-97G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24765 AN: 152146 Hom.: 2205 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0317

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.113 AC: 53 AN: 470 Hom.: 7 AF XY: 0.122 AC XY: 37 AN XY: 304

Gnomad4 AMR exome AF: 0.0208

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.100

Gnomad4 FIN exome AF: 0.0714

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.163 AC: 24779 AN: 152264 Hom.: 2206 Cov.: 33 AF XY: 0.158 AC XY: 11772 AN XY: 74460

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0891

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.152

Alfa AF: 0.151 Hom.: 626

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	7.8
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9261855; hg19: chr6-30383799;