rs60639710

Variant names:

• chr1-198898549-G-T
• rs60639710
• ENST00000436880.2:n.2225C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-198898549-G-T
• chr1-198898549-G-A

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.2225C>A 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 151,810 control chromosomes in the GnomAD database, including 40,262 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.72 (40262 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: -0.376
• 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=-0.8).
• BP6: Variant 1-198898549-G-T is Benign according to our data. Variant chr1-198898549-G-T is described in ClinVar as Benign. ClinVar VariationId is 427754.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.854 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+1862C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR181A1HG	ENST00000436880.2	TSL:1	n.2225C>A		non_coding_transcript_exon	Exon 2 of 2
	MIR181A1HG	ENST00000653207.2		n.463C>A		non_coding_transcript_exon	Exon 3 of 3
	MIR181A1HG	ENST00000665868.3		n.2359C>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109832 AN: 151692 Hom.: 40228 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.701

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: 109921 AN: 151810 Hom.: 40262 Cov.: 32 AF XY: 0.730 AC XY: 54122 AN XY: 74158

African (AFR) AF: 0.820 AC: 34019 AN: 41508

American (AMR) AF: 0.750 AC: 11427 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2699 AN: 3472

East Asian (EAS) AF: 0.792 AC: 4076 AN: 5148

South Asian (SAS) AF: 0.876 AC: 4221 AN: 4820

European-Finnish (FIN) AF: 0.686 AC: 7199 AN: 10498

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

European-Non Finnish (NFE) AF: 0.650 AC: 44078 AN: 67824

Other (OTH) AF: 0.702 AC: 1480 AN: 2108

Alfa AF: 0.681 Hom.: 50364

Bravo AF: 0.727

Asia WGS AF: 0.829 AC: 2857 AN: 3448

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	-0.80
CADD	Benign	8.7
DANN	Benign	0.71
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs60639710; hg19: chr1-198867678;