rs9261850

Variant names:

• chr6-30415635-T-C
• rs9261850

Your query was ambiguous. Multiple possible variants found:

• chr6-30415635-T-C
• chr6-30415635-T-G

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 0.13 in 380,088 control chromosomes in the GnomAD database, including 3,670 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 (2209 hom., cov: 32)
  • Exomes 𝑓: 0.11 (1461 hom.)
• Consequence: MICC intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 13 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

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICC	ENST00000445710.1	TSL:6	n.537+118T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24758 AN: 152062 Hom.: 2208 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0318

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.0889

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.154

GnomAD4 exome AF: 0.108 AC: 24593 AN: 227908 Hom.: 1461 AF XY: 0.109 AC XY: 12933 AN XY: 118664

African (AFR) AF: 0.187 AC: 1351 AN: 7240

American (AMR) AF: 0.0898 AC: 1130 AN: 12582

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 814 AN: 7162

East Asian (EAS) AF: 0.0179 AC: 277 AN: 15478

South Asian (SAS) AF: 0.111 AC: 2634 AN: 23746

European-Finnish (FIN) AF: 0.0653 AC: 761 AN: 11656

Middle Eastern (MID) AF: 0.126 AC: 126 AN: 998

European-Non Finnish (NFE) AF: 0.118 AC: 15952 AN: 135616

Other (OTH) AF: 0.115 AC: 1548 AN: 13430

GnomAD4 genome AF: 0.163 AC: 24772 AN: 152180 Hom.: 2209 Cov.: 32 AF XY: 0.158 AC XY: 11752 AN XY: 74388

African (AFR) AF: 0.238 AC: 9882 AN: 41496

American (AMR) AF: 0.106 AC: 1626 AN: 15306

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

East Asian (EAS) AF: 0.0321 AC: 166 AN: 5178

South Asian (SAS) AF: 0.140 AC: 675 AN: 4818

European-Finnish (FIN) AF: 0.0889 AC: 943 AN: 10606

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

European-Non Finnish (NFE) AF: 0.155 AC: 10532 AN: 67988

Other (OTH) AF: 0.152 AC: 321 AN: 2110

Alfa AF: 0.146 Hom.: 3317

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	7.3
DANN	Benign	0.46
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs9261850; hg19: chr6-30383412;