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GeneBe

rs16873377

Variant summary

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

The ENST00000512563.1(ENSG00000249547):n.138-3910G>A 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 0.133 in 152,038 control chromosomes in the GnomAD database, including 4,438 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 0.13 ( 4438 hom., cov: 32)

Consequence


ENST00000512563.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.05
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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LOC105374524XR_007058437.1 linkuse as main transcriptn.2591+52870C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000512563.1 linkuse as main transcriptn.138-3910G>A intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.133
AC:
20134
AN:
151920
Hom.:
4419
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.456
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0529
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.00187
Gnomad FIN
AF:
0.000283
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.00360
Gnomad OTH
AF:
0.0981
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.133
AC:
20192
AN:
152038
Hom.:
4438
Cov.:
32
AF XY:
0.129
AC XY:
9579
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.457
Gnomad4 AMR
AF:
0.0527
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.00187
Gnomad4 FIN
AF:
0.000283
Gnomad4 NFE
AF:
0.00359
Gnomad4 OTH
AF:
0.0971
Alfa
AF:
0.0788
Hom.:
309
Bravo
AF:
0.150
Asia WGS
AF:
0.0300
AC:
106
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
Cadd
Benign
0.10
Dann
Benign
0.53

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: rs16873377; hg19: chr4-23240591; API