rs2421608

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 0.299 in 152,050 control chromosomes in the GnomAD database, including 8,453 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 ( 8453 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.62
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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.56 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:
0.299
AC:
45408
AN:
151932
Hom.:
8453
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0782
Gnomad AMI
AF:
0.274
Gnomad AMR
AF:
0.320
Gnomad ASJ
AF:
0.410
Gnomad EAS
AF:
0.578
Gnomad SAS
AF:
0.289
Gnomad FIN
AF:
0.478
Gnomad MID
AF:
0.304
Gnomad NFE
AF:
0.374
Gnomad OTH
AF:
0.328
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.299
AC:
45422
AN:
152050
Hom.:
8453
Cov.:
32
AF XY:
0.303
AC XY:
22505
AN XY:
74300
show subpopulations
Gnomad4 AFR
AF:
0.0780
Gnomad4 AMR
AF:
0.320
Gnomad4 ASJ
AF:
0.410
Gnomad4 EAS
AF:
0.577
Gnomad4 SAS
AF:
0.290
Gnomad4 FIN
AF:
0.478
Gnomad4 NFE
AF:
0.374
Gnomad4 OTH
AF:
0.331
Alfa
AF:
0.336
Hom.:
1238
Bravo
AF:
0.278
Asia WGS
AF:
0.354
AC:
1231
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.022
DANN
Benign
0.15

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: rs2421608; hg19: chr2-117297533; COSMIC: COSV60098913; API