rs3997872

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 0.139 in 152,224 control chromosomes in the GnomAD database, including 1,676 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 0.14 ( 1676 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.491
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=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 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

Frequencies

GnomAD3 genomes
AF:
0.139
AC:
21133
AN:
152106
Hom.:
1674
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0897
Gnomad AMI
AF:
0.159
Gnomad AMR
AF:
0.200
Gnomad ASJ
AF:
0.190
Gnomad EAS
AF:
0.0777
Gnomad SAS
AF:
0.0730
Gnomad FIN
AF:
0.141
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.162
Gnomad OTH
AF:
0.126
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.139
AC:
21158
AN:
152224
Hom.:
1676
Cov.:
33
AF XY:
0.138
AC XY:
10235
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.0898
Gnomad4 AMR
AF:
0.201
Gnomad4 ASJ
AF:
0.190
Gnomad4 EAS
AF:
0.0781
Gnomad4 SAS
AF:
0.0731
Gnomad4 FIN
AF:
0.141
Gnomad4 NFE
AF:
0.162
Gnomad4 OTH
AF:
0.125
Alfa
AF:
0.146
Hom.:
224
Bravo
AF:
0.147
Asia WGS
AF:
0.0770
AC:
271
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
5.2
DANN
Benign
0.82

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: rs3997872; hg19: chr6-32580617; API