rs974448

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 0.16 in 152,076 control chromosomes in the GnomAD database, including 2,074 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 0.16 ( 2074 hom., cov: 32)

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=-0.85).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.17 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:
0.161
AC:
24404
AN:
151958
Hom.:
2074
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.142
Gnomad AMI
AF:
0.0811
Gnomad AMR
AF:
0.171
Gnomad ASJ
AF:
0.281
Gnomad EAS
AF:
0.0643
Gnomad SAS
AF:
0.146
Gnomad FIN
AF:
0.154
Gnomad MID
AF:
0.278
Gnomad NFE
AF:
0.172
Gnomad OTH
AF:
0.191
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.160
AC:
24406
AN:
152076
Hom.:
2074
Cov.:
32
AF XY:
0.160
AC XY:
11909
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.142
Gnomad4 AMR
AF:
0.171
Gnomad4 ASJ
AF:
0.281
Gnomad4 EAS
AF:
0.0645
Gnomad4 SAS
AF:
0.145
Gnomad4 FIN
AF:
0.154
Gnomad4 NFE
AF:
0.172
Gnomad4 OTH
AF:
0.189
Alfa
AF:
0.161
Hom.:
262
Bravo
AF:
0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.0
DANN
Benign
0.65

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: rs974448; hg19: chr2-223005314; API