rs1347638

Variant summary

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

The variant allele was found at a frequency of 0.303 in 151,968 control chromosomes in the GnomAD database, including 8,478 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 0.30 ( 8478 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0680
Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.304
AC:
46090
AN:
151848
Hom.:
8470
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.507
Gnomad AMR
AF:
0.285
Gnomad ASJ
AF:
0.378
Gnomad EAS
AF:
0.369
Gnomad SAS
AF:
0.340
Gnomad FIN
AF:
0.300
Gnomad MID
AF:
0.306
Gnomad NFE
AF:
0.417
Gnomad OTH
AF:
0.313
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.303
AC:
46091
AN:
151968
Hom.:
8478
Cov.:
32
AF XY:
0.301
AC XY:
22351
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.284
Gnomad4 ASJ
AF:
0.378
Gnomad4 EAS
AF:
0.370
Gnomad4 SAS
AF:
0.343
Gnomad4 FIN
AF:
0.300
Gnomad4 NFE
AF:
0.417
Gnomad4 OTH
AF:
0.312
Alfa
AF:
0.375
Hom.:
5181
Bravo
AF:
0.292
Asia WGS
AF:
0.335
AC:
1163
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.3
DANN
Benign
0.84

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: rs1347638; hg19: chr15-34941957; API