chr4-68491213-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014058.4(TMPRSS11E):​c.1111-5430G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 145,214 control chromosomes in the GnomAD database, including 8,761 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 0.33 ( 8761 hom., cov: 25)

Consequence

TMPRSS11E
NM_014058.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.639
Variant links:
Genes affected
TMPRSS11E (HGNC:24465): (transmembrane serine protease 11E) Predicted to enable serine-type peptidase activity. Involved in cognition. Predicted to be integral component of plasma membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TMPRSS11ENM_014058.4 linkuse as main transcriptc.1111-5430G>A intron_variant ENST00000305363.9
TMPRSS11EXM_011531896.3 linkuse as main transcriptc.877-5430G>A intron_variant
TMPRSS11EXM_047450139.1 linkuse as main transcriptc.877-5430G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TMPRSS11EENST00000305363.9 linkuse as main transcriptc.1111-5430G>A intron_variant 1 NM_014058.4 P1

Frequencies

GnomAD3 genomes
AF:
0.327
AC:
47459
AN:
145106
Hom.:
8761
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.175
Gnomad AMI
AF:
0.344
Gnomad AMR
AF:
0.340
Gnomad ASJ
AF:
0.460
Gnomad EAS
AF:
0.124
Gnomad SAS
AF:
0.232
Gnomad FIN
AF:
0.321
Gnomad MID
AF:
0.526
Gnomad NFE
AF:
0.425
Gnomad OTH
AF:
0.367
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.327
AC:
47459
AN:
145214
Hom.:
8761
Cov.:
25
AF XY:
0.321
AC XY:
22512
AN XY:
70118
show subpopulations
Gnomad4 AFR
AF:
0.175
Gnomad4 AMR
AF:
0.340
Gnomad4 ASJ
AF:
0.460
Gnomad4 EAS
AF:
0.124
Gnomad4 SAS
AF:
0.232
Gnomad4 FIN
AF:
0.321
Gnomad4 NFE
AF:
0.425
Gnomad4 OTH
AF:
0.369
Alfa
AF:
0.385
Hom.:
3163
Bravo
AF:
0.316
Asia WGS
AF:
0.217
AC:
752
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.2
DANN
Benign
0.68

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs35293564; hg19: chr4-69356931; API