chr6-29745089-T-G

Variant names:

• chr6-29745089-T-G
• rs1633091
• ENST00000510438.1:n.471A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000510438.1(MICE):​n.471A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MICE ENST00000510438.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231
• Publications: 8 publications found

Genes affected

MICE (HGNC:7094): (MHC class I polypeptide-related sequence E (pseudogene))

HLA-F-AS1 (HGNC:26645): (HLA-F antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510438.1. 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
	HLA-F-AS1	NR_026972.1		n.428+2059A>C		intron	N/A
	HLA-F-AS1	NR_026973.1		n.150+3811A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MICE	ENST00000510438.1	TSL:6	n.471A>C		non_coding_transcript_exon	Exon 3 of 6
	HLA-F-AS1	ENST00000849910.1		n.1037A>C		non_coding_transcript_exon	Exon 3 of 4
	HLA-F-AS1	ENST00000399247.6	TSL:6	n.428+2059A>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 214714 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 124784

African (AFR) AF: 0.00 AC: 0 AN: 4758

American (AMR) AF: 0.00 AC: 0 AN: 19022

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4096

East Asian (EAS) AF: 0.00 AC: 0 AN: 8190

South Asian (SAS) AF: 0.00 AC: 0 AN: 34772

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21188

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2242

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 110718

Other (OTH) AF: 0.00 AC: 0 AN: 9728

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.76
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1633091; hg19: chr6-29712866;