2-75274594-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_001739545.2(LOC107985900):​n.30108T>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 0.267 in 152,048 control chromosomes in the GnomAD database, including 5,523 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 0.27 ( 5523 hom., cov: 32)

Consequence

LOC107985900
XR_001739545.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347
Variant links:
Genes affected

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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC107985900XR_001739545.2 linkuse as main transcriptn.30108T>C non_coding_transcript_exon_variant 2/2
LOC105374811NR_168009.1 linkuse as main transcriptn.373-1916A>G intron_variant
LOC105374811NR_168010.1 linkuse as main transcriptn.367-1916A>G intron_variant
LOC107985900XR_001739546.2 linkuse as main transcriptn.29564+4544T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.267
AC:
40611
AN:
151930
Hom.:
5514
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.303
Gnomad AMI
AF:
0.357
Gnomad AMR
AF:
0.276
Gnomad ASJ
AF:
0.184
Gnomad EAS
AF:
0.375
Gnomad SAS
AF:
0.291
Gnomad FIN
AF:
0.342
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.226
Gnomad OTH
AF:
0.254
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.267
AC:
40656
AN:
152048
Hom.:
5523
Cov.:
32
AF XY:
0.273
AC XY:
20296
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.303
Gnomad4 AMR
AF:
0.275
Gnomad4 ASJ
AF:
0.184
Gnomad4 EAS
AF:
0.376
Gnomad4 SAS
AF:
0.292
Gnomad4 FIN
AF:
0.342
Gnomad4 NFE
AF:
0.226
Gnomad4 OTH
AF:
0.259
Alfa
AF:
0.230
Hom.:
5711
Bravo
AF:
0.263
Asia WGS
AF:
0.369
AC:
1284
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
1.9
DANN
Benign
0.74

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: rs9309489; hg19: chr2-75501720; API