2-12599133-T-C

Variant names:

• chr2-12599133-T-C
• rs3731772
• ENST00000414086.1:n.123+24T>C

Variant summary

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

The ENST00000414086.1(ENSG00000223360):​n.123+24T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.897 in 152,252 control chromosomes in the GnomAD database, including 62,516 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 0.90 (62514 hom., cov: 32)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: ENSG00000223360 ENST00000414086.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.715
• Publications: 2 publications found

Genes affected

ENSG00000223360 (HGNC:):

MIR3681HG (HGNC:52001): (MIR3681 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.978 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
ENSG00000223360	ENST00000414086.1	n.123+24T>C		intron_variant	Intron 1 of 3	2
MIR3681HG	ENST00000664018.1	n.578+37868T>C		intron_variant	Intron 4 of 5
MIR3681HG	ENST00000840289.1	n.239+40689T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136557 AN: 152130 Hom.: 62485 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.903

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.897 AC: 136637 AN: 152248 Hom.: 62514 Cov.: 32 AF XY: 0.891 AC XY: 66300 AN XY: 74446

African (AFR) AF: 0.823 AC: 34182 AN: 41522

American (AMR) AF: 0.842 AC: 12872 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3228 AN: 3470

East Asian (EAS) AF: 0.371 AC: 1922 AN: 5176

South Asian (SAS) AF: 0.857 AC: 4132 AN: 4824

European-Finnish (FIN) AF: 0.970 AC: 10291 AN: 10608

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.984 AC: 66970 AN: 68036

Other (OTH) AF: 0.900 AC: 1902 AN: 2114

Alfa AF: 0.940 Hom.: 8239

Bravo AF: 0.883

Asia WGS AF: 0.667 AC: 2321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.78
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs3731772; hg19: chr2-12739259;