7-12883931-T-C

Variant summary

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

The ENST00000638964.1(ENSG00000229618):​n.484+81199T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,728 control chromosomes in the GnomAD database, including 24,950 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 0.56 ( 24950 hom., cov: 30)

Consequence

ENSG00000229618
ENST00000638964.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.92
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 (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENSG00000229618ENST00000638964.1 linkn.484+81199T>C intron_variant 5
ENSG00000229618ENST00000639998.1 linkn.483+125615T>C intron_variant 5

Frequencies

GnomAD3 genomes
AF:
0.560
AC:
84853
AN:
151610
Hom.:
24918
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.765
Gnomad AMI
AF:
0.280
Gnomad AMR
AF:
0.507
Gnomad ASJ
AF:
0.453
Gnomad EAS
AF:
0.491
Gnomad SAS
AF:
0.467
Gnomad FIN
AF:
0.519
Gnomad MID
AF:
0.617
Gnomad NFE
AF:
0.474
Gnomad OTH
AF:
0.558
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.560
AC:
84920
AN:
151728
Hom.:
24950
Cov.:
30
AF XY:
0.561
AC XY:
41578
AN XY:
74100
show subpopulations
Gnomad4 AFR
AF:
0.765
Gnomad4 AMR
AF:
0.506
Gnomad4 ASJ
AF:
0.453
Gnomad4 EAS
AF:
0.490
Gnomad4 SAS
AF:
0.467
Gnomad4 FIN
AF:
0.519
Gnomad4 NFE
AF:
0.474
Gnomad4 OTH
AF:
0.554
Alfa
AF:
0.513
Hom.:
2492
Bravo
AF:
0.565
Asia WGS
AF:
0.523
AC:
1816
AN:
3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.35
DANN
Benign
0.52

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: rs6460985; hg19: chr7-12923556; API