rs9261854

chr6-30415898-T-C

Variant summary

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

The ENST00000445710.1(MICC):n.538-221T>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 0.163 in 152,130 control chromosomes in the GnomAD database, including 2,204 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 (2204 hom., cov: 32)
• Consequence: MICC ENST00000445710.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

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=-0.95).
• 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.538-221T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24747 AN: 152012 Hom.: 2203 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0313

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.163 AC: 24761 AN: 152130 Hom.: 2204 Cov.: 32 AF XY: 0.158 AC XY: 11765 AN XY: 74410

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0316

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0888

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.152

Alfa AF: 0.146 Hom.: 412

Bravo AF: 0.170

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	6.0
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261854; hg19: chr6-30383675;