rs9261855

Variant names:

• chr6-30416022-G-A
• rs9261855

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 152,734 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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.959
• Publications: 15 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=-0.97).
• 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 rank	MANE	Protein	UniProt
MICC		n.30416022G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MICC	ENST00000445710.1	n.538-97G>A		intron_variant	Intron 2 of 4	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.0208 AC: 1 AN: 48

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AF: 0.100 AC: 1 AN: 10

European-Finnish (FIN) AF: 0.0714 AC: 1 AN: 14

Middle Eastern (MID) AF: 0.167 AC: 1 AN: 6

European-Non Finnish (NFE) AF: 0.124 AC: 47 AN: 378

Other (OTH) AF: 0.100 AC: 1 AN: 10

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

African (AFR) AF: 0.238 AC: 9882 AN: 41520

American (AMR) AF: 0.106 AC: 1626 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3472

East Asian (EAS) AF: 0.0320 AC: 166 AN: 5186

South Asian (SAS) AF: 0.141 AC: 679 AN: 4822

European-Finnish (FIN) AF: 0.0891 AC: 946 AN: 10618

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10532 AN: 68016

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

Alfa AF: 0.158 Hom.: 1395

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
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs9261855; hg19: chr6-30383799;