2-12701319-T-G

Position:

• chr2-12701319-T-G

Variant summary

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

The XR_007086221.1(LOC124905974):​n.3591A>C 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 0.532 in 151,958 control chromosomes in the GnomAD database, including 22,049 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 0.53 (22049 hom., cov: 32)
• Consequence: LOC124905974 XR_007086221.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646

Genes affected

LOC124905974 (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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124905974	XR_007086221.1	n.3591A>C		non_coding_transcript_exon_variant	2/2
LOC124905974	XR_007086222.1	n.11280A>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3681HG	ENST00000664018.1	n.698-778T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80836 AN: 151840 Hom.: 22041 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.532 AC: 80887 AN: 151958 Hom.: 22049 Cov.: 32 AF XY: 0.538 AC XY: 39931 AN XY: 74262

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.538

Alfa AF: 0.494 Hom.: 3246

Bravo AF: 0.536

Asia WGS AF: 0.677 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.1
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs645490; hg19: chr2-12841445;