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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445710.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICC	ENST00000445710.1	TSL:6	n.538-97G>A		intron	N/A

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 v4.9

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;