2-12601191-G-T

Position:

• chr2-12601191-G-T

Variant summary

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

The ENST00000414086.1(ENSG00000223360):​n.124-1257G>T variant causes a intron, non coding transcript 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: ENST00000414086.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

Genes affected

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000414086.1	n.124-1257G>T		intron_variant, non_coding_transcript_variant		2
MIR3681HG	ENST00000664018.1	n.578+39926G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.970

Gnomad4 NFE AF: 0.984

Gnomad4 OTH AF: 0.899

Alfa AF: 0.960 Hom.: 136553

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1519543; hg19: chr2-12741317;