chr1-198781293-C-T

Variant names:

• chr1-198781293-C-T
• rs12568099
• ENST00000660348.1:n.356-1990G>A

Variant summary

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

The ENST00000660348.1(MIR181A1HG):​n.356-1990G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0295 in 152,064 control chromosomes in the GnomAD database, including 208 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 0.029 (208 hom., cov: 32)
• Consequence: MIR181A1HG ENST00000660348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR181A1HG	ENST00000660348.1	n.356-1990G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0294 AC: 4473 AN: 151946 Hom.: 209 Cov.: 32

Gnomad AFR AF: 0.00747

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.0593

Gnomad FIN AF: 0.00728

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0311

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0295 AC: 4479 AN: 152064 Hom.: 208 Cov.: 32 AF XY: 0.0306 AC XY: 2272 AN XY: 74300

Gnomad4 AFR AF: 0.00745

Gnomad4 AMR AF: 0.0679

Gnomad4 ASJ AF: 0.0121

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.0598

Gnomad4 FIN AF: 0.00728

Gnomad4 NFE AF: 0.0215

Gnomad4 OTH AF: 0.0322

Alfa AF: 0.0339 Hom.: 30

Bravo AF: 0.0360

Asia WGS AF: 0.144 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12568099; hg19: chr1-198750422;