11-1207997-C-T

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 0.366 in 152,120 control chromosomes in the GnomAD database, including 10,944 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 0.37 ( 10944 hom., cov: 33)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0920
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 (AFR) allele frequency at 95% confidence interval = 0.503 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:
0.366
AC:
55608
AN:
152002
Hom.:
10928
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.509
Gnomad AMI
AF:
0.270
Gnomad AMR
AF:
0.429
Gnomad ASJ
AF:
0.294
Gnomad EAS
AF:
0.249
Gnomad SAS
AF:
0.322
Gnomad FIN
AF:
0.263
Gnomad MID
AF:
0.297
Gnomad NFE
AF:
0.299
Gnomad OTH
AF:
0.342
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.366
AC:
55673
AN:
152120
Hom.:
10944
Cov.:
33
AF XY:
0.365
AC XY:
27164
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.509
Gnomad4 AMR
AF:
0.429
Gnomad4 ASJ
AF:
0.294
Gnomad4 EAS
AF:
0.250
Gnomad4 SAS
AF:
0.321
Gnomad4 FIN
AF:
0.263
Gnomad4 NFE
AF:
0.299
Gnomad4 OTH
AF:
0.339
Alfa
AF:
0.333
Hom.:
2416
Bravo
AF:
0.385
Asia WGS
AF:
0.327
AC:
1134
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
2.3
DANN
Benign
0.72

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: rs28654232; hg19: chr11-1229227; COSMIC: COSV65940574; API