ENST00000436880.2:n.1819C>T

Variant names:

• chr1-198898955-G-A
• rs10800597
• ENST00000436880.2:n.1819C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000436880.2(MIR181A1HG):​n.1819C>T 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 0.724 in 151,930 control chromosomes in the GnomAD database, including 40,351 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.72 (40351 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: MIR181A1HG ENST00000436880.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts P:1 B:2
• Conservation: PhyloP100: -0.819
• Publications: 2 publications found

Genes affected

MIR181A1HG (HGNC:48659): (MIR181A1 host gene)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 1-198898955-G-A is Benign according to our data. Variant chr1-198898955-G-A is described in ClinVar as Benign. ClinVar VariationId is 427755.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000436880.2. 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
	MIR181A1HG	NR_040073.1		n.363+1456C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR181A1HG	ENST00000436880.2	TSL:1	n.1819C>T		non_coding_transcript_exon	Exon 2 of 2
	MIR181A1HG	ENST00000665868.3		n.1953C>T		non_coding_transcript_exon	Exon 2 of 2
	MIR181A1HG	ENST00000432296.2	TSL:3	n.363+1456C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109963 AN: 151812 Hom.: 40313 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.702

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.724 AC: 110059 AN: 151930 Hom.: 40351 Cov.: 32 AF XY: 0.730 AC XY: 54176 AN XY: 74210

African (AFR) AF: 0.822 AC: 34088 AN: 41478

American (AMR) AF: 0.751 AC: 11451 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2698 AN: 3470

East Asian (EAS) AF: 0.792 AC: 4070 AN: 5140

South Asian (SAS) AF: 0.874 AC: 4220 AN: 4828

European-Finnish (FIN) AF: 0.683 AC: 7199 AN: 10542

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44124 AN: 67906

Other (OTH) AF: 0.704 AC: 1485 AN: 2110

Alfa AF: 0.700 Hom.: 4840

Bravo AF: 0.728

Asia WGS AF: 0.831 AC: 2884 AN: 3470

ClinVar

ClinVar submissions as Germline

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
1	-	-	Acute myeloblastic leukemia with maturation (1)
-	-	1	not provided (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.9
DANN	Benign	0.66
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs10800597; hg19: chr1-198868084;