rs9261854

Variant names:

• chr6-30415898-T-C
• rs9261854

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MICC		n.30415898T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICC	ENST00000445710.1	n.538-221T>C		intron_variant	Intron 2 of 4	6

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

African (AFR) AF: 0.238 AC: 9877 AN: 41484

American (AMR) AF: 0.106 AC: 1625 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3470

East Asian (EAS) AF: 0.0316 AC: 163 AN: 5162

South Asian (SAS) AF: 0.140 AC: 678 AN: 4826

European-Finnish (FIN) AF: 0.0888 AC: 942 AN: 10608

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.155 AC: 10530 AN: 67964

Other (OTH) AF: 0.152 AC: 321 AN: 2114

Alfa AF: 0.146 Hom.: 2169

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
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs9261854; hg19: chr6-30383675;