rs718768

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 0.751 in 152,196 control chromosomes in the GnomAD database, including 43,310 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 0.75 ( 43310 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0250
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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 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

Frequencies

GnomAD3 genomes
AF:
0.751
AC:
114212
AN:
152078
Hom.:
43250
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.805
Gnomad AMI
AF:
0.701
Gnomad AMR
AF:
0.769
Gnomad ASJ
AF:
0.663
Gnomad EAS
AF:
0.937
Gnomad SAS
AF:
0.778
Gnomad FIN
AF:
0.710
Gnomad MID
AF:
0.655
Gnomad NFE
AF:
0.711
Gnomad OTH
AF:
0.727
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.751
AC:
114334
AN:
152196
Hom.:
43310
Cov.:
33
AF XY:
0.754
AC XY:
56120
AN XY:
74396
show subpopulations
Gnomad4 AFR
AF:
0.805
Gnomad4 AMR
AF:
0.769
Gnomad4 ASJ
AF:
0.663
Gnomad4 EAS
AF:
0.936
Gnomad4 SAS
AF:
0.778
Gnomad4 FIN
AF:
0.710
Gnomad4 NFE
AF:
0.711
Gnomad4 OTH
AF:
0.730
Alfa
AF:
0.711
Hom.:
49235
Bravo
AF:
0.757
Asia WGS
AF:
0.859
AC:
2985
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.9
DANN
Benign
0.43

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: rs718768; hg19: chr4-110824115; COSMIC: COSV69025164; API