chr2-23191780-A-G

Variant summary

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

The NR_171639.1(LOC107985792):​n.121+7029T>C 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 0.261 in 152,146 control chromosomes in the GnomAD database, including 5,533 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 0.26 ( 5533 hom., cov: 32)

Consequence

LOC107985792
NR_171639.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550
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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC107985792NR_171639.1 linkuse as main transcriptn.121+7029T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000669447.1 linkuse as main transcriptn.121+7029T>C intron_variant, non_coding_transcript_variant
ENST00000440785.1 linkuse as main transcriptn.248+7029T>C intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.261
AC:
39627
AN:
152028
Hom.:
5535
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.202
Gnomad AMI
AF:
0.183
Gnomad AMR
AF:
0.204
Gnomad ASJ
AF:
0.177
Gnomad EAS
AF:
0.0963
Gnomad SAS
AF:
0.272
Gnomad FIN
AF:
0.329
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.317
Gnomad OTH
AF:
0.233
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.261
AC:
39651
AN:
152146
Hom.:
5533
Cov.:
32
AF XY:
0.258
AC XY:
19183
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.202
Gnomad4 AMR
AF:
0.203
Gnomad4 ASJ
AF:
0.177
Gnomad4 EAS
AF:
0.0960
Gnomad4 SAS
AF:
0.270
Gnomad4 FIN
AF:
0.329
Gnomad4 NFE
AF:
0.317
Gnomad4 OTH
AF:
0.235
Alfa
AF:
0.292
Hom.:
12271
Bravo
AF:
0.246
Asia WGS
AF:
0.218
AC:
758
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
4.0
DANN
Benign
0.76

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: rs1449984; hg19: chr2-23414651; API