chr19-56848064-T-C

Variant names:

• chr19-56848064-T-C
• rs373361
• ENST00000599641.2:n.847T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000599641.2(MIMT1):​n.847T>C 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 0.93 in 152,294 control chromosomes in the GnomAD database, including 65,988 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 0.93 (65986 hom., cov: 31)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: MIMT1 ENST00000599641.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 2 publications found

Genes affected

MIMT1 (HGNC:33464): (MER1 repeat containing imprinted transcript 1)

ENSG00000274777 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIMT1	NR_024059.2	n.798T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIMT1	ENST00000599641.2	n.847T>C		non_coding_transcript_exon_variant	Exon 2 of 2	1
MIMT1	ENST00000652034.1	n.687T>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000274777	ENST00000614523.1	n.-4T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.930 AC: 141516 AN: 152172 Hom.: 65928 Cov.: 31

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.907

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.930 AC: 141633 AN: 152290 Hom.: 65986 Cov.: 31 AF XY: 0.932 AC XY: 69360 AN XY: 74450

African (AFR) AF: 0.975 AC: 40559 AN: 41578

American (AMR) AF: 0.932 AC: 14251 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2948 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5178 AN: 5184

South Asian (SAS) AF: 0.965 AC: 4651 AN: 4822

European-Finnish (FIN) AF: 0.931 AC: 9872 AN: 10606

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61250 AN: 68020

Other (OTH) AF: 0.907 AC: 1918 AN: 2114

Alfa AF: 0.911 Hom.: 114992

Bravo AF: 0.931

Asia WGS AF: 0.981 AC: 3413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.78
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs373361; hg19: chr19-57359432;