1-198900385-T-C

Variant names:

• chr1-198900385-T-C
• rs10800598
• ENST00000436880.2:n.389A>G

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.389A>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 0.743 in 151,980 control chromosomes in the GnomAD database, including 42,796 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.74 (42795 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: MIR181A1HG ENST00000436880.2 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts P:1 B:2
• Conservation: PhyloP100: -0.427
• 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=-0.83).
• BP6: Variant 1-198900385-T-C is Benign according to our data. Variant chr1-198900385-T-C is described in ClinVar as Benign. ClinVar VariationId is 427756.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR181A1HG	NR_040073.1		n.363+26A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR181A1HG	ENST00000436880.2	TSL:1	n.389A>G		non_coding_transcript_exon	Exon 2 of 2
	MIR181A1HG	ENST00000665868.3		n.523A>G		non_coding_transcript_exon	Exon 2 of 2
	MIR181A1HG	ENST00000806898.1		n.590A>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112889 AN: 151860 Hom.: 42751 Cov.: 31

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.713

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 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) AC: 0 AN: 0

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: 0.743 AC: 112993 AN: 151978 Hom.: 42795 Cov.: 31 AF XY: 0.749 AC XY: 55589 AN XY: 74246

African (AFR) AF: 0.879 AC: 36496 AN: 41532

American (AMR) AF: 0.758 AC: 11549 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2707 AN: 3470

East Asian (EAS) AF: 0.829 AC: 4256 AN: 5132

South Asian (SAS) AF: 0.877 AC: 4225 AN: 4818

European-Finnish (FIN) AF: 0.684 AC: 7218 AN: 10556

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.652 AC: 44305 AN: 67912

Other (OTH) AF: 0.714 AC: 1510 AN: 2114

Alfa AF: 0.691 Hom.: 10295

Bravo AF: 0.750

Asia WGS AF: 0.850 AC: 2956 AN: 3478

ClinVar

ClinVar submissions

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	-0.83
CADD	Benign	5.4
DANN	Benign	0.77
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs10800598; hg19: chr1-198869514;