rs12596341

Variant summary

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

The ENST00000646214.1(ENSG00000285163):​n.77+8374C>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 0.0802 in 152,186 control chromosomes in the GnomAD database, including 672 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 0.080 ( 672 hom., cov: 31)

Consequence


ENST00000646214.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.776
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=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ENST00000646214.1 linkuse as main transcriptn.77+8374C>A intron_variant, non_coding_transcript_variant
ENST00000645383.1 linkuse as main transcriptn.393+1160C>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0802
AC:
12202
AN:
152068
Hom.:
669
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0203
Gnomad AMI
AF:
0.222
Gnomad AMR
AF:
0.0787
Gnomad ASJ
AF:
0.158
Gnomad EAS
AF:
0.174
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.0625
Gnomad MID
AF:
0.0981
Gnomad NFE
AF:
0.105
Gnomad OTH
AF:
0.0952
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0802
AC:
12201
AN:
152186
Hom.:
672
Cov.:
31
AF XY:
0.0789
AC XY:
5867
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.0202
Gnomad4 AMR
AF:
0.0785
Gnomad4 ASJ
AF:
0.158
Gnomad4 EAS
AF:
0.174
Gnomad4 SAS
AF:
0.101
Gnomad4 FIN
AF:
0.0625
Gnomad4 NFE
AF:
0.105
Gnomad4 OTH
AF:
0.0985
Alfa
AF:
0.0859
Hom.:
98
Bravo
AF:
0.0791
Asia WGS
AF:
0.118
AC:
410
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
2.1
DANN
Benign
0.33

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: rs12596341; hg19: chr16-85967040; API