chr2-111366168-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000451884.6(MIR4435-2HG):​n.215A>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 0.00205 in 152,322 control chromosomes in the GnomAD database, including 6 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 0.0021 ( 6 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MIR4435-2HG
ENST00000451884.6 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.45
Variant links:
Genes affected
MIR4435-2HG (HGNC:35163): (MIR4435-2 host gene)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00205 (313/152322) while in subpopulation EAS AF= 0.0209 (108/5174). AF 95% confidence interval is 0.0177. There are 6 homozygotes in gnomad4. There are 197 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MIR4435-2HGNR_015395.2 linkn.1685A>C non_coding_transcript_exon_variant 2/7
MIR4435-2HGNR_136162.1 linkn.1685A>C non_coding_transcript_exon_variant 2/5
MIR4435-2HGNR_136166.1 linkn.1685A>C non_coding_transcript_exon_variant 2/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MIR4435-2HGENST00000439362.6 linkn.273+1319A>C intron_variant 1
MIR4435-2HGENST00000451884.6 linkn.215A>C non_coding_transcript_exon_variant 1/53
MIR4435-2HGENST00000643013.1 linkn.1644A>C non_coding_transcript_exon_variant 2/6

Frequencies

GnomAD3 genomes
AF:
0.00206
AC:
314
AN:
152204
Hom.:
6
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00458
Gnomad ASJ
AF:
0.00950
Gnomad EAS
AF:
0.0208
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.00602
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000367
Gnomad OTH
AF:
0.00239
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
36
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
26
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00205
AC:
313
AN:
152322
Hom.:
6
Cov.:
30
AF XY:
0.00265
AC XY:
197
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.0000722
Gnomad4 AMR
AF:
0.00457
Gnomad4 ASJ
AF:
0.00950
Gnomad4 EAS
AF:
0.0209
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.00602
Gnomad4 NFE
AF:
0.000367
Gnomad4 OTH
AF:
0.00236
Alfa
AF:
0.000635
Hom.:
0
Bravo
AF:
0.00196
Asia WGS
AF:
0.0110
AC:
37
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.72
CADD
Benign
16
DANN
Benign
0.87

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2292932; hg19: chr2-112123745; API