chr2-12601191-G-T

Variant names:

• chr2-12601191-G-T
• rs1519543
• ENST00000414086.1:n.124-1257G>T

Variant summary

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

The ENST00000414086.1(ENSG00000223360):​n.124-1257G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,248 control chromosomes in the GnomAD database, including 62,365 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 (62365 hom., cov: 33)
• Consequence: ENSG00000223360 ENST00000414086.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309
• Publications: 1 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=-1.0).
• 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.124-1257G>T		intron_variant	Intron 1 of 3	2
MIR3681HG	ENST00000664018.1	n.578+39926G>T		intron_variant	Intron 4 of 5
MIR3681HG	ENST00000840289.1	n.239+42747G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136374 AN: 152130 Hom.: 62336 Cov.: 33

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.896 AC: 136454 AN: 152248 Hom.: 62365 Cov.: 33 AF XY: 0.889 AC XY: 66213 AN XY: 74452

African (AFR) AF: 0.819 AC: 34004 AN: 41514

American (AMR) AF: 0.841 AC: 12863 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3230 AN: 3472

East Asian (EAS) AF: 0.370 AC: 1913 AN: 5170

South Asian (SAS) AF: 0.856 AC: 4132 AN: 4826

European-Finnish (FIN) AF: 0.970 AC: 10307 AN: 10624

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

European-Non Finnish (NFE) AF: 0.984 AC: 66969 AN: 68036

Other (OTH) AF: 0.899 AC: 1898 AN: 2112

Alfa AF: 0.949 Hom.: 209301

Bravo AF: 0.881

Asia WGS AF: 0.665 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.56
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs1519543; hg19: chr2-12741317;