6-29745089-T-C

Position:

• chr6-29745089-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000510438.1(MICE):​n.471A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 366,810 control chromosomes in the GnomAD database, including 134,401 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 0.81 (50540 hom., cov: 33)
  • Exomes 𝑓: 0.88 (83861 hom.)
• Consequence: MICE ENST00000510438.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HLA-F-AS1	NR_026973.1	n.150+3811A>G		intron_variant, non_coding_transcript_variant
HLA-F-AS1	NR_026972.1	n.428+2059A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MICE	ENST00000510438.1	n.471A>G		non_coding_transcript_exon_variant	3/6
HLA-F-AS1	ENST00000458236.1	n.349+384A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123514 AN: 152052 Hom.: 50478 Cov.: 33

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.816

GnomAD4 exome AF: 0.882 AC: 189377 AN: 214640 Hom.: 83861 Cov.: 0 AF XY: 0.888 AC XY: 110731 AN XY: 124740

Gnomad4 AFR exome AF: 0.858

Gnomad4 AMR exome AF: 0.937

Gnomad4 ASJ exome AF: 0.929

Gnomad4 EAS exome AF: 0.988

Gnomad4 SAS exome AF: 0.951

Gnomad4 FIN exome AF: 0.746

Gnomad4 NFE exome AF: 0.871

Gnomad4 OTH exome AF: 0.870

GnomAD4 genome AF: 0.812 AC: 123634 AN: 152170 Hom.: 50540 Cov.: 33 AF XY: 0.811 AC XY: 60309 AN XY: 74396

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.818

Alfa AF: 0.818 Hom.: 26167

Bravo AF: 0.823

Asia WGS AF: 0.938 AC: 3263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1633091; hg19: chr6-29712866;